US11203611B2 - Immunomodulating polynucleotides, antibody conjugates thereof, and methods of their use - Google Patents

Immunomodulating polynucleotides, antibody conjugates thereof, and methods of their use Download PDF

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US11203611B2
US11203611B2 US15/953,290 US201815953290A US11203611B2 US 11203611 B2 US11203611 B2 US 11203611B2 US 201815953290 A US201815953290 A US 201815953290A US 11203611 B2 US11203611 B2 US 11203611B2
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oligonucleotide
group
cpg
optionally substituted
cell
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US20180312536A1 (en
Inventor
Sukumar Sakamuri
Curt W. Bradshaw
Son Lam
Joseph STOCK
Edward HyungSuk Ha
Laxman Eltepu
Dingguo Liu
Bin Liu
Giuseppe Dello IACONO
Bryan R. Meade
Ayman Kabakibi
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Tallac Therapeutics Inc
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Tollnine Inc
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Assigned to TOLLNINE, INC. reassignment TOLLNINE, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: SOLSTICE BIOLOGICS, LTD.
Assigned to SOLSTICE BIOLOGICS, LTD. reassignment SOLSTICE BIOLOGICS, LTD. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: LAM, SON, LIU, DINGGUO, ELTEPU, LAXMAN, KABAKIBI, AYMAN, HA, EDWARD HYUNGSUK, MEADE, BRYAN R., IACONO, GIUSEPPE DELLO, STOCK, JOSEPH, BRADSHAW, CURT W., SAKAMURI, SUKUMAR, LIU, BIN
Assigned to TOLLNINE, INC. reassignment TOLLNINE, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: SOLSTICE BIOLOGICS LIMITED
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    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
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    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
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    • C12N2310/51—Physical structure in polymeric form, e.g. multimers, concatemers

Definitions

  • This invention relates to compositions and methods for modulating the immune system response.
  • an immunomodulating polynucleotide is also provided herein.
  • an immunomodulating polynucleotide comprising a 5-modified uridine or a 5-modified cytidine and having a length ranging from about 6 to about 16 nucleotides.
  • a conjugate comprising a targeting moiety and one or more immunomodulating polynucleotides.
  • a pharmaceutical composition comprising an immunomodulating polynucleotide or a conjugate comprising a targeting moiety and one or more immunomodulating polynucleotides.
  • PAMPs Pathogen-associated molecular patterns
  • TLRs toll-like receptors
  • PRRs pattern recognition receptors
  • the ability of PAMPs to recruit immune system in the absence of pathogens provides a strategy for treating a variety of diseases involving cell destruction (e.g., anticancer therapy) through the use of innate immune system response.
  • One class of PAMPs that has been investigated for a variety of therapeutic applications is immunostimulating polynucleotides, such as CpG ODN (e.g., agatolimod).
  • CpG ODNs mediate TLR9 dimerization in immune cells (e.g., B cells, monocytes, and plasmacytoid dendritic cells (pDCs)) to upregulate cytokines (e.g., type I interferon and interleukins), thereby activating natural killer cells.
  • immune cells e.g., B cells, monocytes, and plasmacytoid dendritic cells (pDCs)
  • cytokines e.g., type I interferon and interleukins
  • CpG ODNs are generally divided into three classes: class A, class B, and class C.
  • Class A CpG ODNs typically contain poly-G tails with phosphorothioate backbones at 3′- and 5′-termini and a central palindromic sequence including a phosphate backbone.
  • Class A CpG ODNs typically contain CpG within the central palindrome sequence.
  • Class B CpG ODNs typically include fully phosphorothioate backbone, and the sequence at the 5′ end of class B CpG ODN is often critical for TLR9 activation.
  • Class C CpG ODNs include fully phosphorothioate backbone with a 3′-end sequence enabling formation of a duplex.
  • CpG ODNs are often susceptible to degradation in serum. Thus, pharmacokinetics of CpG ODNs may be one of the limiting factors in their development as therapeutics. Further, CpG ODNs often exhibit uneven tissue distribution in vivo, with primary sites of accumulation being in liver, kidney, and spleen. Such distribution can elicit off-target activity and local toxicity associated with PAMPs. Thus, therapeutic applications of CpG ODNs may be facilitated by addressing the pharmacokinetic/pharmacodynamic challenges described herein.
  • the present invention relates to immunomodulating (e.g., immunostimulating) polynucleotides and conjugates containing a targeting moiety and one or more immunomodulating (e.g., immunostimulating) polynucleotides.
  • immunomodulating polynucleotides may be an immunostimulating polynucleotide.
  • the immunomodulating polynucleotide may be an immunosuppressive polynucleotide.
  • the immunomodulating polynucleotide contains one or more (e.g., 1 or 2) abasic spacers or phosphotriesters. In particular embodiments, the immunomodulating polynucleotide contains one or more (e.g., 1 to 5) internucleoside phosphotriesters. In further embodiments, at least one of the internucleoside phosphotriesters contains a conjugating group. In yet further embodiments, the immunomodulating polynucleotide further contains a terminal phosphoester (e.g., a 5′-terminal phosphoester or 3′-terminal phosphoester). In still further embodiments, the terminal phosphoester contains a conjugating group.
  • a terminal phosphoester e.g., a 5′-terminal phosphoester or 3′-terminal phosphoester. In still further embodiments, the terminal phosphoester contains a conjugating group.
  • the immunomodulating polynucleotide includes a 5′-cap or 3′-cap. In yet other embodiments, the immunomodulating polynucleotide contains the 5′-cap that is a 5′-5′ cap. In still other embodiments, the 5′-5′ cap contains a conjugating group covalently bonded to an internucleoside phosphate, internucleoside phosphorothioate, or internucleoside phosphorodithioate.
  • the immunomodulating polynucleotide includes the 3′-cap containing a conjugating group covalently bonded to an internucleoside phosphate, internucleoside phosphorothioate, or internucleoside phosphorodithioate.
  • the immunomodulating polynucleotide contains a 5′-capping group that is monophosphate, diphosphate, triphosphate, an auxiliary moiety, a terminal phosphodiester, a terminal phosphotriester, a 5′-5′ cap, or a group —OR′, where R′ is a bioreversible group, a non-bioreversible group, or an O-protecting group.
  • the 5′-capping group is monophosphate or the terminal phosphodiester including optionally substituted C 1-6 alkyl bonded to phosphate, phosphorothioate, or phosphorodithioate.
  • the immunomodulating polynucleotide contains a 3′-capping group that is monophosphate, diphosphate, triphosphate, an auxiliary moiety, a terminal phosphodiester, a terminal phosphotriester, and a group —OR′, where R′ is a bioreversible group, a non-bioreversible group, or an O-protecting group.
  • the 3′-capping group is monophosphate or the terminal phosphodiester comprising optionally substituted C 1-6 alkyl bonded to phosphate, phosphorothioate, or phosphorodithioate.
  • the immunomodulating polynucleotide contains one or more (e.g., 1 or 2) abasic spacers.
  • at least one of the abasic spacers is an internucleoside abasic spacer.
  • at least one of the abasic spacers is a 3′-terminal abasic spacer.
  • at least one of the abasic spacers comprises a conjugating group.
  • the immunomodulating polynucleotide contains a 5-modified uridine (e.g., 5-halouridine (e.g., 5-bromouridine or 5-iodouridine) or 5-modified cytidine).
  • a 5-modified uridine e.g., 5-halouridine (e.g., 5-bromouridine or 5-iodouridine) or 5-modified cytidine.
  • the 5-modified uridine e.g., 5-halouridine (e.g., 5-bromouridine or 5-iodouridine)
  • ISS immunostimulating sequence
  • the 5-modified uridine (e.g., 5-halouridine) includes a 3′-position bonded to an internucleoside phosphodiester phosphate.
  • the 5-modified uridine (e.g., 5-halouridine) includes a 3′-position bonded to an internucleoside phosphodiester phosphorothioate.
  • the 5-modified uridine (e.g., 5-halouridine) is 5′-terminal.
  • the 5-modified uridine is 5-bromouridine.
  • the immunomodulating polynucleotide contains cytidine and guanosine as the second and third nucleosides or as the third and fourth nucleosides.
  • the immunomodulating polynucleotide contains a 5′-terminal immunostimulating sequence.
  • at least one of the internucleoside phosphotriesters is bonded to a 3′-carbon atom of a nucleoside having a 5′-carbon atom which is bonded to a 5′-terminal immunostimulating sequence.
  • the immunomodulating polynucleotide comprises a total of from 6 to 16 (e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16) nucleotides.
  • at least 10% (e.g., at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%) of internucleoside bridging groups in the immunomodulating polynucleotide contain phosphorothioates.
  • at least 50% of internucleoside bridging groups in the immunomodulating polynucleotide contain phosphorothioates.
  • the immunomodulating polynucleotide includes a conjugating group covalently bonded to a nucleobase in the immunomodulating polynucleotide.
  • the immunomodulating polynucleotide includes one or more auxiliary moieties.
  • the immunomodulating polynucleotide includes a conjugating moiety containing at least one of the auxiliary moieties.
  • at least of the one auxiliary moieties contains a polyethylene glycol) (PEG) having a molecular weight of from 100 Da to 2,500 Da.
  • PEG polyethylene glycol
  • each PEG contains independently a total of at least 3 ethylene glycol repeating units.
  • each PEG contains independently a total of at least 20 ethylene glycol repeating units.
  • each PEG contains independently a total of 50 or fewer ethylene glycol repairing units.
  • the immunomodulating polynucleotide contains from one to eight PEGs.
  • the immunomodulating polynucleotide is a polynucleotide disclosed herein (e.g., in Table 2).
  • hybridized immunomodulating polynucleotides containing an immunomodulating polynucleotide hybridized to a complementary polynucleotide.
  • compositions containing an immunomodulating polynucleotide in which the immunomodulating polynucleotide contains at least one stereochemically enriched internucleoside phosphorothioate.
  • At least one stereochemically enriched internucleoside phosphorothioate is disposed between a 5′-terminal nucleoside and cytidine of CpG in an immunostimulating sequence in the immunomodulating polynucleotide.
  • one stereochemically enriched internucleoside phosphorothioate connects the first and the second nucleosides in the immunomodulating polynucleotide.
  • one stereochemically enriched internucleoside phosphorothioate is bonded to 5′-carbon atom of cytidine of CpG in an immunostimulating sequence in the immunomodulating polynucleotide.
  • one stereochemically enriched internucleoside phosphorothioate connects the fourth and the fifth nucleosides in the immunomodulating polynucleotide.
  • the stereochemically enriched internucleoside phosphorothioate is S-stereogenic.
  • the stereochemically enriched internucleoside phosphorothioate is R-stereogenic.
  • conjugates containing a targeting moiety and one or more immunomodulating polynucleotides.
  • the targeting moiety is an antigen-binding moiety, a polypeptide, an aptamer, or a group including one or more small molecules.
  • the targeting moiety is an antigen-binding moiety (e.g., an antibody or an antigen-binding fragment thereof).
  • the antibody or the antibody fragment includes an N-terminal or C-terminal Q-tag, where the immunomodulating polynucleotide(s) are independently covalently bonded to the N-terminal or C-terminal Q-tag.
  • the Q-tag is disposed in a heavy chain or light chain of the antibody or the antibody fragment.
  • the immunomodulating polynucleotide is as disclosed in other aspects.
  • At least one of the immunomodulating polynucleotides contains a 5-modified uridine or 5-modified cytidine.
  • at least one of the immunomodulating polynucleotides comprises a 5-modified uridine that is 5-halouridine, 5-alkynyluridine, or 5-heterocyclyluridine.
  • the 5-modified uridine is 5-halouridine (e.g., 5-bromouridine or 5-iodouridine).
  • the 5-modified uridine is one of two 5′-terminal nucleotides of at least one of the immunomodulating polynucleotides.
  • the 5-modified uridine comprises a 3′-position bonded to an internucleoside phosphoester phosphate. In yet other embodiments, the 5-modified uridine comprises a 3′-position bonded to an internucleoside phosphoester phosphorothioate. In still other embodiments, at least one of the immunomodulating polynucleotides contains cytidine and guanosine as the second and third nucleosides. In particular embodiments, at least one of the immunomodulating polynucleotides contains cytidine and guanosine as the third and fourth nucleosides.
  • At least one of the immunomodulating polynucleotides contains a total of from 6 to 16 (e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16) nucleotides.
  • At least one of the immunomodulating polynucleotides contains one or more abasic spacers or internucleoside phosphotriesters. In yet further embodiments, at least one abasic spacer or at least one phosphotriester contains the linker.
  • At least one of the immunomodulating polynucleotides contains one or more (e.g., 1 or 2) abasic spacers.
  • at least one of the abasic spacers is an internucleoside abasic spacer.
  • at least one of the abasic spacers is a 3′-terminal abasic spacer.
  • At least one of the immunomodulating polynucleotides contains one or more (e.g., 1 to 5) internucleoside phosphotriesters.
  • the conjugate further contains one or more auxiliary moieties bonded to the linker.
  • at least of the one auxiliary moieties contains a polyethylene glycol) (PEG) having a molecular weight of from 100 Da to 2,500 Da.
  • PEG polyethylene glycol
  • each PEG independently contains a total of at least 3 (e.g., at least 5, at least 6, at least, 7 at least 8, at least 9, at least 10, at least 12, at least 14, at least 16, at least 18, or at least 20) ethylene glycol repeating units.
  • each PEG independently contains a total of 50 or fewer (e.g., 45 or fewer, 40 or fewer, 35 or fewer, or 30 or fewer) ethylene glycol repearing units.
  • the conjugate contains from one to eight PEGs.
  • a 5′-capping group in at least one of the immunomodulating polynucleotides is monophosphate, diphosphate, triphosphate, an auxiliary moiety, a terminal phosphodiester, a terminal phosphotriester, or a group-OR′, where R′ is a bioreversible group, a non-bioreversible group, or an O-protecting group.
  • the 5′-capping group is monophosphate or the terminal phosphodiester containing optionally substituted C 1-6 alkyl bonded to phosphate, phosphorothioate, or phosphorodithioate.
  • the 3′-capping group in at least one of the immunomodulating polynucleotides is monophosphate, diphosphate, triphosphate, an auxiliary moiety, a terminal phosphodiester, a terminal phosphotriester, or a group —OR′, where R′ is a bioreversible group, a non-bioreversible group, or an O-protecting group.
  • the 3′-capping group is monophosphate or the terminal phosphodiester containing optionally substituted C 1-6 alkyl bonded to phosphate, phosphorothioate, or phosphorodithioate.
  • At least one of immunomodulating polynucleotides contains a nucleobase bonded to the linker.
  • the conjugate contains from one to six (e.g., 1 to 4) immunomodulating polynucleotides. In yet further embodiments, the conjugate contains only one immunomodulating polynucleotide. In still further embodiments, the conjugate contains only two immunomodulating polynucleotides. In other embodiments, the conjugate contains one targeting moiety.
  • the immunomodulating polynucleotide contains a human immunostimulating sequence within four 5′-terminal nucleotides.
  • the human immunostimulating sequence within four 5′-terminal nucleotides of the immunomodulating polynucleotide includes cytidine containing a 5′-carbon atom bonded to a phosphoester substituted with a nucleoside.
  • At least one of the immunomodulating polynucleotides contains a 5-modified uridine or 5-modified cytidine.
  • At least one of the immunomodulating polynucleotides is hybridized to its complement.
  • At least one of the immunomodulating polynucleotides contains at least one stereochemically enriched internucleoside phosphorothioate.
  • At least one stereochemically enriched internucleoside phosphorothioate is disposed between a 5′-terminal nucleoside and cytidine of CpG in an immunostimulating sequence in the immunomodulating polynucleotide.
  • at least one stereochemically enriched internucleoside phosphorothioate is bonded to 5′-carbon atom of cytidine of CpG in an immunostimulating sequence in the immunomodulating polynucleotide.
  • at least one stereochemically enriched internucleoside phosphorothioate connects the first and the second nucleosides in the immunomodulating polynucleotide.
  • At least one stereochemically enriched internucleoside phosphorothioate connects the fourth and the fifth nucleosides in the immunomodulating polynucleotide.
  • the stereochemically enriched internucleoside phosphorothioate is S-stereogenic.
  • the stereochemically enriched internucleoside phosphorothioate is R-stereogenic.
  • compositions containing a pharmaceutically acceptable carrier and the immunomodulating polynucleotide of invention, the stereochemically enriched composition of the invention, or the conjugate of the invention.
  • a cell comprising the endosomal toll-like receptor by contacting the cell with the immunomodulating polynucleotide of the invention, the composition of the invention, the conjugate of the invention, or the pharmaceutical composition of the invention under conditions permitting the immunomodulating polynucleotides to be transported into the cell, where, after the contacting, the activity of the endosomal toll-like receptor is modulated.
  • the immunomodulating polynucleotide is an immunostimulating polynucleotide
  • the method is for agonizing an endosomal toll-like receptor.
  • the immunomodulating polynucleotide is an immunosuppressive polynucleotide
  • the method is for antagonizing an endosomal toll-like receptor.
  • cytokines inducing one or more cytokines in an antigen-presenting cell containing an endosomal toll-like receptor by contacting the antigen-presenting cell with the immunomodulating polynucleotide of the invention, the composition of the invention, the conjugate of the invention, or the pharmaceutical composition of the invention under conditions permitting the one or more immunomodulating polynucleotides to be transported into the cell, where, after the contacting, the level of at least one cytokine in the cell is increased, where the targeting moiety targets the antigen-presenting cell, and where the immunomodulating polynucleotide is an immunostimulating polynucleotide.
  • the antigen-presenting cell is a B cell.
  • at least one of the one or more cytokines is an inflammatory cytokine.
  • the antigen-presenting cell is a plasmacytoid dendritic cell, and where the targeting moiety targets the plasmacytoid dendritic cell.
  • the antigen-presenting cell is a macrophage.
  • at least one of the cytokines is a type I interferon.
  • the toll-like receptor is TLR9.
  • a liquid tumor in a patient by administering to the patient an effective amount of the immunomodulating polynucleotide of the invention, the composition of the invention, the conjugate of the invention, or the pharmaceutical composition of the invention, where the targeting moiety targets B cells, and where the immunomodulating polynucleotide is an immunostimulating polynucleotide that is a TLR9 agonist.
  • the liquid tumor is a hematologic tumor (e.g., the hematologic tumor is a lymphoma).
  • the lymphoma is a non-Hodgkin B-cell lymphoma.
  • the lymphoma is mantle cell lymphoma, diffuse large B cell lymphoma, follicular lymphoma, chronic lymphocytic leukemia, or multiple myeloma.
  • the method for treating a solid tumor in a patient comprises administering to the patient an immunomodulating polynucleotide as disclosed herein, wherein the immunomodulating polynucleotide targets B cell in the patient.
  • the present invention also provides uses of the immunomodulating polynucleotides of the invention, conjugates of the invention, compositions of the invention, or pharmaceutical compositions of the invention in the manufacture of products (e.g., medicaments) for the purposes described herein (e.g., for treating a liquid or solid tumor in a patient). It is also to be understood that the present invention also provides uses of the immunomodulating polynucleotides of the invention, conjugates of the invention, compositions of the invention, or pharmaceutical compositions of the invention for the purposes described herein (e.g., for treating a liquid or solid tumor in a patient).
  • the present invention also provides the immunomodulating polynucleotides of the invention, conjugates of the invention, compositions of the invention, or pharmaceutical compositions of the invention for use according to the purposes described herein (e.g., for treating a liquid or solid tumor in a patient).
  • the linker can be as disclosed herein (e.g., according to any one of formulae (II), (V), and (VI)-(XV)).
  • the conjugating group can be as disclosed herein.
  • each X N is independently a nucleotide
  • X 3′ is a 3′ terminal nucleotide
  • X 5′ is a 5′ terminal nucleotide
  • Y P is an internucleoside phosphotriester
  • b and c are each an integer ranging from about 0 to about 25; with the proviso that their sum is no less than 5;
  • oligonucleotide comprises a nucleotide with a modified nucleobase.
  • an oligonucleotide having a sequence of N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T (SEQ ID NO: 497), or a stereoisomer, a mixture of two or more diastereomers, a tautomer, or a mixture of two or more tautomers thereof; or a pharmaceutically acceptable salt, solvate, or hydrate thereof; wherein:
  • x is an integer ranging from 1 to 4.
  • N 1 is absent or 2′-deoxythymidine
  • N 2 is a 2′-deoxyribonucleotide with a modified nucleobase
  • N 3 is 2′-deoxyadenosine or 2′-deoxythymidine, each optionally comprising a 3′-phosphotriester;
  • N 4 is 2′-deoxyadenosine or 2′-deoxythymidine
  • N 5 is 2′-deoxythymidine optionally comprising a 3′-phosphotriester.
  • R x is a conjugating group
  • L N is a linker
  • each Q is independently an oligonucleotide comprising a phosphotriester
  • e is an integer of 1, 2, 3, or 4.
  • Ab is an antibody
  • each L N is independently a linker
  • each Q is independently an oligonucleotide comprising a phosphotriester
  • each e is independently an integer of 1, 2, 3, or 4;
  • f is an integer of 1, 2, 3, or 4.
  • kits for treating cancer in a subject having cancer comprising administering a therapeutically effective amount of a CpG-Ab immunoconjugate to the subject, wherein the CpG-Ab immunoconjugate does not bind to a tumor associated antigen (TAA).
  • TAA tumor associated antigen
  • the CpG-Ab immunoconjugate specifically binds to a target antigen associated with a normal immune cell that expresses at least one toll-like receptor.
  • the normal immune cell expresses TLR9.
  • the normal immune cell is an antigen presenting cell (APC).
  • the APC is a B cell, a dendritic cells or a macrophage.
  • the target antigen is selected from the group consisting of a MHC molecule, a T cell costimulatory molecule, an immune checkpoint molecule, a B cell specific antigen, a dendritic cell specific antigen and a macrophage specific antigen.
  • the MHC molecule is selected from MHC class I and MHC class II molecules.
  • the T cell costimulatory molecule is selected from the list consisting of OX40, CD2, CD27, CDS, ICAM-1, LFA-1/CD11a/CD18, ICOS/CD278, 4-1BB/CD137, GITR, CD30, CD40, BAFFR, HVEM, CD7, LIGHT, NKG2C, SLAMF7, NKp80, CD160, B7-H3, and CD83.
  • the immune checkpoint molecule is selected from the list consisting of PD-1, PD-L1, PD-L2, TIM-1, TIM-3, LAG-3, CEACAM-1, CEACAM-5, CLTA-4, VISTA, BTLA, TIGIT, LAIR1, CD47, CD160, 2B4, CD172a, and TGF ⁇ .
  • target antigen is selected from the group consisting of CD1, CD2, CD3, CD5, CD6, CD9, CD11, CD14, CD17, CD18, CD19, CD20, CD21, CD22, CD23, CD24, CD25, CD26, CD27, CD30, CD32, CD37, CD38, CD39, CD40, CD44, CD45R (B220), CD49, CD52, CD55, CD56, CD64, CD66 (Carcinoembrionic antigen, CEA), CD68, CD70, CD74, CD79b, CD80, CD93, CD115, CD123, CD126, CD127, CD137, CD138, CD163, CD196, CD197, CD200R, CD205, CD206, CD207, CD208, CD209, CD267, CD269, CD274, CD300a, CD301, CD303, CD304, CD319, CD336, CLEC5a, CLEC6, CLEC9a, CXCL16, CX3CR1, and DC-STAMP.
  • the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from Table 2. In some embodiments, the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from the group consisting of p236, p238, p243, p246, p275, p276, p308, p313, p347, p361, p362, p425, p433, p434, p435, p436, p437, p438, p477, p478, p479, p480, p481, p482, p483, p484, p485, p486, p487, p488 and p489.
  • the CpG-Ab immunoconjugates is not conjugated to a T cell epitope.
  • the T cell epitope is an epitope of ovalbumin (OVA).
  • OVA ovalbumin
  • the cancer is a solid tumor.
  • the cancer is a liquid tumor.
  • the administering or co-administering is through systemic administration.
  • the therapeutic effective amount of the CpG-Ab immunoconjugate is not effective to activate the complement pathway in the subject. In some embodiments of the methods provided herein, the amount is not effective to activate complement C3 in the subject.
  • methods of treating cancer in a subject having cancer comprises administering a therapeutically effective amount of a CpG-Ab immunoconjugate to the subject, wherein the CpG-Ab immunoconjugate specifically binds to a tumor associated antigen (TAA), wherein the TAA is not an antigen selected from the group consisting of CD19, CD20, CD22, exportin 7, Her2, Src, EGFR, CD52, CXCR-4, Muc-1 and DNA.
  • TAA tumor associated antigen
  • binding of the CpG-Ab immunoconjugate to the TAA facilitates internalization of the CpG-Ab immunoconjugate into a cancer cell expressing the TAA.
  • binding of the CpG-Ab immunoconjugate to the TAA facilitates transportation of the CpG-Ab immunoconjugate to endosome of the cancer cell expressing the TAA. In some embodiments, binding of the CpG-Ab immunoconjugate to the TAA facilitates activation of a TLR9 signaling pathway in a cancer cell expressing the TAA. In some embodiments, the TAA and the TLR9 are located on a same cellular membrane of the cancer cell expressing the TAA. In some embodiments, both the TAA and the TLR9 are located on the cell membrane of the cancer cell expressing the TAA. In some embodiments, both the TAA and the TLR9 are located on the endosomal membrane of the cancer cell expressing the TAA.
  • binding of the CpG-Ab immunoconjugate to the TAA induces apoptosis of the cancer cell expressing the TAA.
  • the TAA is not expressed by a normal immune cell.
  • the TAA is expressed by a normal immune cell.
  • the normal immune cell is an antigen presenting cell (APC).
  • the TAA is selected from the group consisting of CD8, CD11 b, CD11c, CD14, CD33, CD40, CD123, CD157, CD168, CD169, CD172a, CD200, CD204, CD205, CD301, CD302, CD303, CD304, and CD206.
  • the CpG-Ab immunoconjugate is not conjugated to the TAA or any other TAA expressed by the cancer.
  • the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from Table 2.
  • the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from the group consisting of p236, p238, p243, p246, p275, p276, p308, p313, p347, p361, p362, p425, p433, p434, p435, p436, p437, p438, p477, p478, p479, p480, p481, p482, p483, p484, p485, p486, p487, p488 and p489.
  • an immunostimulating polynucleotide selected from the group consisting of p236, p238, p243, p246, p275, p276, p308, p313, p347, p361, p362, p425, p433, p434, p435, p436, p437, p
  • the CpG-Ab immunoconjugate is not conjugated to a T cell epitope.
  • the T cell epitope is ovalbumin (OVA).
  • OVA ovalbumin
  • the cancer is a solid tumor.
  • the cancer is a liquid tumor.
  • the cancer is recurrent cancer.
  • the administering or co-administering is through systemic administration.
  • the therapeutic effective amount of the CpG-Ab immunoconjugate is not effective to activate the complement pathway in the subject. In some embodiments of the methods provided herein, the amount is not effective to activate complement C3 in the subject.
  • kits for treating an immunotherapy resistant or refractory cancer in a subject having immunotherapy resistant or refractory cancer comprising administering a therapeutically effective amount of a CpG-Ab immunoconjugate to the subject.
  • the CpG-Ab immunoconjugate does not bind to a tumor associated antigen.
  • the CpG-Ab immunoconjugate specifically binds to a target antigen associated with a normal immune cell that expresses at least one toll-like receptor.
  • the CpG-Ab immunoconjugate specifically binds to a tumor associated antigen.
  • the cancer is resistant to treatment with an immune checkpoint modulator.
  • the method further comprising co-administering to the subject the immune checkpoint modulator.
  • the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from Table 2.
  • the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from the group consisting of p236, p238, p243, p246, p275, p276, p308, p313, p347, p361, p362, p425, p433, p434, p435, p436, p437, p438, p477, p478, p479, p480, p481, p482, p483, p484, p485, p486, p487, p488 and p489 as shown in Table 2.
  • the cancer is a solid tumor. In some embodiments the cancer is a liquid tumor. In some embodiments of the methods provided herein, the cancer is recurrent cancer. In some embodiments of the methods provided herein, the administering or co-administering is through systemic administration. In some embodiments of the methods provided herein, the therapeutic effective amount of the CpG-Ab immunoconjugate is not effective to activate the complement pathway in the subject. In some embodiments of the methods provided herein, the amount is not effective to activate complement C3 in the subject.
  • kits for preventing cancer in a subject in need thereof comprising administering a therapeutically effective amount of a CpG-Ab immunoconjugate to the subject, wherein the CpG-Ab immunoconjugate specifically binds to a target antigen associated with a normal immune cell expressing at least one toll-like receptor.
  • such method further comprises co-administering a tumor associated antigen with the CpG-Ab immunoconjugate.
  • the CpG-Ab immunoconjugate is not conjugated to the tumor associated antigen.
  • the normal immune cell expresses TLR9.
  • the normal immune cell is an antigen presenting cell (APC).
  • the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from Table 2. In some embodiments, the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from the group consisting of p236, p238, p243, p246, p275, p276, p308, p313, p347, p361, p362, p425, p433, p434, p435, p436, p437, p438, p477, p478, p479, p480, p481, p482, p483, p484, p485, p486, p487, p488 and p489 as shown in Table 2.
  • the cancer is a solid tumor. In some embodiments the cancer is a liquid tumor. In some embodiments of the methods provided herein, the cancer is recurrent cancer. In some embodiments of the methods provided herein, the administering or co-administering is through systemic administration. In some embodiments of the methods provided herein, the therapeutic effective amount of the CpG-Ab immunoconjugate is not effective to activate the complement pathway in the subject. In some embodiments of the methods provided herein, the amount is not effective to activate complement C3 in the subject.
  • provided herein are methods of preventing cancer in a subject in need thereof, comprising co-administering a therapeutic effective amount of a CpG-Ab immunoconjugate with a cancer vaccine, wherein the CpG-Ab immunoconjugate specifically binds to a target antigen associated with a normal immune cell expressing at least one toll-like receptor.
  • the CpG-Ab immunoconjugate is formulated as an adjuvant of the cancer vaccine.
  • the cancer is a solid tumor.
  • the cancer is a liquid tumor.
  • the cancer is recurrent cancer.
  • the administering or co-administering is through systemic administration.
  • the therapeutic effective amount of the CpG-Ab immunoconjugate is not effective to activate the complement pathway in the subject. In some embodiments of the methods provided herein, the amount is not effective to activate complement C3 in the subject.
  • kits for inducing an adaptive immune response in a subject comprising administering a therapeutically effective amount of a CpG-Ab immunoconjugate to the subject, wherein the CpG-Ab immunoconjugate specifically binds to a target antigen associated with a normal immune cell expressing at least one toll-like receptor.
  • the subject has cancer.
  • the target antigen is not a TAA.
  • the target antigen is a TAA that is not an antigen selected from the group consisting of CD19, CD20, CD22, STAT3, exportin 7, Her2, Src, EGFR, CD52, CXCR-4, Muc-1 and DNA.
  • the subject has an infectious disease.
  • the normal immune cell expresses TLR9.
  • the normal immune cell is an antigen presenting cell (APC).
  • the adaptive immune response is CD8+ T cell dependent.
  • the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from Table 2.
  • the CpG-Ab immunoconjugates comprises an immunostimulating polynucleotide selected from the group consisting of p236, p238, p243, p246, p275, p276, p308, p313, p347, p361, p362, p425, p433, p434, p435, p436, p437, p438, p477, p478, p479, p480, p481, p482, p483, p484, p485, p486, p487, p488 and p489 as shown in Table 2.
  • the cancer is a solid tumor.
  • the cancer is a liquid tumor. In some embodiments of the methods provided herein, the cancer is recurrent cancer. In some embodiments of the methods provided herein, the administering or co-administering is through systemic administration. In some embodiments of the methods provided herein, the therapeutic effective amount of the CpG-Ab immunoconjugate is not effective to activate the complement pathway in the subject. In some embodiments of the methods provided herein, the amount is not effective to activate complement C3 in the subject.
  • kits for treating cancer in a subject having cancer comprising administering to the subject a therapeutic effective amount of a CpG-Ab immunoconjugates selected from Table 6.
  • the CpG-Ab immunoconjugates binds to a tumor associated antigen (TAA).
  • TAA tumor associated antigen
  • the CpG-Ab immunoconjugates binds to a target antigen other than the TAA.
  • the CpG-Ab immunoconjugates binds to the target antigen associated with a normal immune cell expressing a TLR receptor.
  • the CpG-Ab immunoconjugates is selected from the group consisting of CpG-Ab immunoconjugates comprisingp 236, p238, p243, p246, p275, p276, p308, p313, p347, p361, p362, p425, p433, p434, p435, p436, p437, p438, p477, p478, p479, p480, p481, p482, p483, p484, p485, p486, p487, p488 and p489 as shown in Table 2.
  • the at least one additional cancer therapeutic agent is selected from a second TAA, a T cell costimulatory molecule, and an immune checkpoint modulator.
  • the second TAA is the same as the TAA. In some embodiments, the second TAA is different from the TAA.
  • the T cell costimulatory molecule is selected from the list consisting of OX40, CD2, CD27, CDS, ICAM-1, LFA-1/CD11a/CD18, ICOS/CD278, 4-1BB/CD137, GITR, CD30, CD40, BAFFR, HVEM, CD7, LIGHT, NKG2C, SLAMF7, NKp80, CD160, B7-H3, and CD83 or an ligand thereof.
  • the T cell costimulatory molecule is an anti-OX40 antibody, anti-ICOS/CD278 antibody or anti-4-1 BB/CD137 antibody, or an antigen-binding fragment thereof.
  • the immune checkpoint modulator is an inhibitor of immune checkpoint molecules selected from the list consisting of PD-1, PD-L1, PD-L2, TIM-3, LAG-3, CEACAM-1, CEACAM-5, CLTA-4, VISTA, BTLA, TIGIT, LAIR1, CD47, CD160, 2B4, CD172a, and TGFR.
  • the immune checkpoint modulator is an anti-CD47 antibody, anti-PD-1 antibody, anti-PD-L1 antibody, or an antigen-binding fragment thereof.
  • the cancer is a solid tumor. In some embodiments the cancer is a liquid tumor. In some embodiments of the methods provided herein, the cancer is recurrent cancer.
  • the administering or co-administering is through systemic administration.
  • the therapeutic effective amount of the CpG-Ab immunoconjugate is not effective to activate the complement pathway in the subject. In some embodiments of the methods provided herein, the amount is not effective to activate complement C3 in the subject.
  • the CpG-Ab immunoconjugate comprises an oligonucleotide of Formula (A) as defined above. In some embodiments of any of the methods provided herein, wherein the CpG-Ab immunoconjugate comprises a compound of Formula (B) as defined above. In some embodiments of any of the methods provided herein, wherein the CpG-Ab immunoconjugate is a compound of Formula (C) as defined above.
  • FIG. 1A is a series of structures showing abbreviations with corresponding structures. The abbreviations are those used in Table 2.
  • FIG. 1B is a series of structures showing abbreviations with corresponding structures. The abbreviations are those used in Table 2.
  • FIG. 2 is an image of an ethidium bromide-stained denaturing gel of single-stranded CpG ODNs (lanes A (p145) and D (p88)) and annealed double-stranded CpG ODNs (lanes B (p88/p144) and C (p88/p145)).
  • FIG. 3A is an image of ethidium bromide-stained reducing gels of a Q-tagged anti-CD38 antibody before (lane A) and after mouse transglutaminase-mediated conjugation with a polynucleotide (p76, p77, p78, p79, p80, p81, and p82 corresponding to lanes B, C, D, E, F, G, and H, respectively.
  • HC+1 indicates bands of a Q-tagged anti-CD38 antibody heavy chain conjugated to a polynucleotide.
  • HC indicates bands of a Q-tagged anti-CD38 antibody heavy chain.
  • LC indicates an anti-CD38 antibody light chain.
  • FIG. 3B is an image of ethidium bromide-stained reducing gels of a Q-tagged anti-CD38 antibody before (lane A) and after microbial transglutaminase-mediated conjugation with a polynucleotide p83, p84, p85, p86, p87, and p88 corresponding to lanes B, C, D, E, F, and G, respectively.
  • HC+1 indicates bands of a Q-tagged anti-CD38 antibody heavy chain conjugated to a polynucleotide.
  • HC indicates bands of a Q-tagged anti-CD38 antibody heavy chain.
  • LC indicates an anti-CD38 antibody light chain.
  • FIG. 4A is an image of an ethidium bromide-stained denaturing gel of a Q-tagged anti-CD38 conjugated to an azide linker before (lane A) and after conjugation through dipolar cycloaddition to a single-stranded polynucleotide (lane B, a Dari conjugate with p88) or to a double-stranded polynucleotide (lanes C, D, E, and F).
  • Lane C corresponds to the isolated first AEX peak for the conjugate of Q-tagged anti-CD38 antibody linked by a metal-free 1,3-dipolar cycloaddition to p88/p145 double-stranded CpG.
  • Lane D corresponds to the isolated second AEX peak for the conjugate of Q-tagged anti-CD38 antibody linked by a metal-free 1,3-dipolar cycloaddition to p88/p145 double-stranded CpG.
  • Lane E corresponds to the isolated first AEX peak for the conjugate of Q-tagged anti-CD38 antibody linked by a metal-free 1,3-dipolar cycloaddition to p88/p144 double-stranded CpG.
  • Lane F corresponds to the isolated second AEX peak for the conjugate of Q-tagged anti-CD38 antibody linked by a metal-free 1,3-dipolar cycloaddition to p88/p144 double-stranded CpG.
  • FIG. 4B is a graph showing AEX-HPLC traces for a crude mixture containing rituximab-p19 conjugate showing signals based on absorbance at 280 nm and at 260 nm. There are three peaks corresponding to rituximab-p19 conjugate.
  • FIG. 4C is a graph showing a composite of AEX-HPLC traces for: the crude mixture, p19, and rituximab-p19 AEX peaks 1, 2, and 3, which are enumerated in FIG. 4B .
  • FIG. 4D is an image of a denaturing SDS PAGE 6% tris-glycine gel comparing rituximab-PEG24-N3 (lane A), crude conjugation reaction mixture (lane B), and isolated rituximab-p19 AEX peaks 1 (lane C), 2 (lane D), and 3 (lane E).
  • FIG. 5 is a graph showing the efficacy of the murine immunostimulating polynucleotides to induce IL-6 dose-dependently in murine splenocytes.
  • the illustrated data indicate that, for murine immunostimulating polynucleotide sequence of p18, at least 15 phosphorothioates are preferable to achieve immunostimulating activity.
  • a phosphorothioate backbone is an important feature controlling the efficacy of immunostimulating polynucleotides to induce IL-6.
  • FIG. 6 is a graph showing the efficacy of the immunoconjugates of the invention and CpG 7909 in the activation of NF ⁇ B dose-dependently in Ramos Blue cells, as measured by the levels of alkaline phosphatases after 5.5 h of treatment.
  • the x-axis provides the concentration (nM) of the conjugate on the log scale.
  • FIG. 7 is a graph showing the efficacy of the immunoconjugates and CpG 7909 in the activation of NF ⁇ B dose-dependently in Ramos Blue cells, as measured by the levels of alkaline phosphatases after 24 h of treatment and 2.5 h of QB incubation.
  • the xaxis provides log of the concentration (M) of the conjugates on the linear scale.
  • FIG. 8 is a graph showing the efficacy of the immunoconjugates in the activation of NF ⁇ B dose-dependently in Ramos Blue cells, as measured by the levels of alkaline phosphatases after 48 h of treatment and 2.5 h of QB incubation.
  • the xaxis provides log of the concentration (M) of the conjugates on the linear scale.
  • FIG. 9 is a graph comparing the efficacy of p1 and p6 polynucleotides in the activation of NF ⁇ B dose-dependently in Ramos Blue cells, as measured by the levels of alkaline phosphatases.
  • FIG. 10 is a graph showing the efficacy of the immunoconjugates in the activation of NF ⁇ B dose-dependently in Ramos Blue cells, as measured by the levels of alkaline phosphatases.
  • FIG. 11 is a graph showing the efficacy of the immunoconjugates in the activation of NF ⁇ B dose-dependently in Ramos Blue cells, as measured by the levels of alkaline phosphatases.
  • FIG. 12 is a graph showing the efficacy of the immunoconjugates in the activation of NF ⁇ B dose-dependently in Ramos Blue cells, as measured by the levels of alkaline phosphatases.
  • FIG. 13 is a graph showing the efficacy of the immunoconjugates in the activation of NF ⁇ B dose-dependently in Ramos Blue cells, as measured by the levels of alkaline phosphatases.
  • FIG. 14 is a graph showing the efficacy of the immunoconjugates in the activation of NF ⁇ B dose-dependently in Ramos Blue cells, as measured by the levels of alkaline phosphatases.
  • FIG. 15 is a graph showing the efficacy of the immunoconjugates in the dose-dependent induction of IL-6 in DB cells.
  • the y-axis shows the multiplier for the increase of IL6 secretion normalized to PPIB levels.
  • FIG. 16 is a graph showing the efficacy of the immunoconjugates in the dose-dependent induction of NF ⁇ B in Ramos Blue cells. This figure compares the conjugates having one polynucleotide (Dari) or two polynucleotides (Dar2) to activate NF ⁇ B.
  • FIG. 17 is a graph showing the efficacy of the immunoconjugates in the dose-dependent induction of IL-6 in DB cells. This figure compares the conjugates having one polynucleotide (Dari) or two polynucleotides (Dar2) to induce IL6. The y-axis shows the multiplier for the increase of IL6 secretion normalized to PPIB levels.
  • FIG. 18 is a graph showing the efficacy of the immunoconjugates containing immunostimulating polynucleotides of varying length in activating NF ⁇ B in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 19 is a graph showing the efficacy of the immunoconjugates containing immunostimulating polynucleotides of varying length in activating NF ⁇ B in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 20 is a graph showing the comparison of the immunostimulating activity of conjugates containing polynucleotides with 5′-terminal 5-iodo-2-deoxyuridine that is bonded to an internucleoside phosphodiester phosphate to the immunostimulating activity of conjugates containing polynucleotides with 5′-terminal 5-iodo-2-deoxyuridine that is bonded to an internucleoside phosphodiester phosphorothioate.
  • the immunostimulating activities were assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 21 is a graph showing the comparison of the immunostimulating activity of conjugates containing polynucleotides with 5′-terminal 5-iodo-2-deoxyuridine that is bonded to an internucleoside phosphodiester phosphate to the immunostimulating activity of conjugates containing polynucleotides with 5′-terminal 5-iodo-2-deoxyuridine that is bonded to an internucleoside phosphodiester phosphorothioate.
  • the immunostimulating activities were assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 22 is a graph showing the comparison of the immunostimulating activities of conjugates containing one or more 5-iodo-2-deoxyuridines.
  • the immunostimulating activities were assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 23 is a graph showing the comparison of the immunostimulating activities of conjugates containing or lacking 5-iodo-2-deoxyuridine.
  • the immunostimulating activities were assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 24 is a graph showing the comparison of immunostimulating activities of conjugates containing internucleoside phosphotriesters that are phosphate-based or phosphorothioate-based. The immunostimulating activity was assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 25 is a graph showing the comparison of immunostimulating activities of conjugates containing internucleoside phosphotriesters that are phosphate-based or phosphorothioate-based. The immunostimulating activity was assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 26A is a graph showing the comparison of immunostimulating activities of conjugates containing one or more phosphorothioate-based internucleoside phosphotriesters.
  • the immunostimulating activity was assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 26B is a graph showing the comparison of immunostimulating activities of conjugates containing one or more phosphorothioate-based internucleoside phosphotriesters.
  • the immunostimulating activity was assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 27 is a graph showing the comparison of immunostimulating activities of conjugates containing an antibody and one or more immunostimulating polynucleotides.
  • the immunostimulating activity was assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • FIG. 28 is a graph showing the comparison of cellular dependent cytotoxicity (CDC) of immunostimulating polynucleotides conjugated through a heavy chain Q-tag or a light chain Q-tag in an antibody.
  • the CDC assay was performed in Daudi cells incubated with the conjugates in human sera, and the cytotoxicity was measured by fluorescence.
  • FIG. 29 is a graph showing the comparison of immunostimulating activities of conjugates having auxiliary moieties.
  • the immunostimulating activity was assessed through the measurement of the NF ⁇ B activation in Ramos-Blue cells, as measured by alkaline phosphatase readout.
  • the designator in parenthesis indicates the linker/auxiliary moiety structure used in the conjugate, no AM indicates that conjugate SB-189 does not contain an auxiliary moiety.
  • FIG. 30 is a graph showing the comparison of CDC activities of conjugates having auxiliary moieties.
  • the CDC assay was performed in Daudi cells incubated with the conjugates in human sera, and the cytotoxicity was measured by fluorescence.
  • FIG. 31 is a graph showing the induction of IL6 in A20 mouse B-cell lymphoma cells using conjugates containing a truncated murine cross-reactive human immunostimulating polynucleotide (p275) linked through a Q-tag to a murine anti-CD22 antibody.
  • p275 truncated murine cross-reactive human immunostimulating polynucleotide
  • FIG. 32 is a graph showing the induction of IL6 in A20 mouse B-cell lymphoma cells using conjugates containing a truncated murine cross-reactive human immunostimulating polynucleotide (p275) linked through a Q-tag to a murine anti-CD22 antibody.
  • p275 truncated murine cross-reactive human immunostimulating polynucleotide
  • FIG. 33A is a graph showing the induction of IL6 in A20 mouse B-cell lymphoma cells using conjugates containing immunostimulating polynucleotides or an unconjugated immunostimulating polynucleotide.
  • FIG. 33B is a graph showing the induction of IL6 in A20 mouse B-cell lymphoma cells by conjugates containing an anti-mouse CD22 antibody and an immunostimulating polynucleotide in the presence of varying concentration of the free anti-mouse CD22 antibody.
  • FIG. 34A is a graph showing the induction of interferon- ⁇ in human PBMC by CpG-2336, a class A CpG ODN.
  • FIG. 34B is a graph showing the induction of interferon- ⁇ in human PBMC using conjugate SB-340.
  • Anti-BDCA2 antibody, SB-341, and p246 were used as controls in this experiment.
  • the Y-axis provides optical density in arbitrary units at the wavelength of 450 nm.
  • FIG. 34C is a graph showing the induction of interferon- ⁇ in purified plasmacytoid cells using conjugate SB-342.
  • Anti-BDCA2 antibody, anti-BDCA4 antibody, and SB-343 were used as controls in this experiment.
  • FIG. 35 is a graph showing the comparison of immunostimulatory activity of the polynucleotides with various 5′-terminal modifications and internucleoside triesters.
  • FIG. 36 is a graph showing the comparison of immunostimulatory activity of the polynucleotides with various 5′-terminal modifications and internucleoside triesters.
  • FIG. 37A is a graph showing tumor volume growth progression following inoculation of a mouse with A20 mouse B-cell lymphoma cells and the subsequent, triple, intratumoral administration of a vehicle (saline) or an immunostimulating polynucleotide of the invention (p326) and a control (p18). The administration times are indicated with the arrows on the X-axis.
  • FIG. 37B is a graph showing tumor volume growth progression following inoculation of a mouse with A20 mouse B-cell lymphoma cells and the subsequent, triple, intravenous administration of a vehicle (saline), an immunostimulating polynucleotide (p3), an anti-CD22 antibody (CD22), or conjugates SB-338, SB-339, or SB-344.
  • vehicle saline
  • p3 immunostimulating polynucleotide
  • CD22 anti-CD22 antibody
  • conjugates SB-338, SB-339, or SB-344 conjugates SB-338, SB-339, or SB-344.
  • FIG. 38A is a graph showing tumor volume growth progression following inoculation of a mouse with A20 mouse B-cell lymphoma cells and the subsequent, triple, intratumoral administration of a vehicle (saline) or an immunostimulating polynucleotide.
  • FIG. 38B is a graph showing tumor volume values on day 20 after the inoculation of a mouse with A20 mouse B-cell lymphoma cells and the subsequent, triple, intratumoral administration of a vehicle (saline) or an immunostimulating polynucleotide.
  • FIG. 39A is a graph showing tumor volume growth progression following the inoculation of a mouse with A20 mouse B-cell lymphoma cells and (i) the subsequent, single, intravenous administration of a conjugate of the invention (SB-337), or (ii) the subsequent, triple, intratumoral administration of a vehicle (saline) or an immunostimulating polynucleotide.
  • FIG. 39B is a graph showing tumor volume values on day 20 after the inoculation of a mouse with A20 mouse B-cell lymphoma cells and (i) the subsequent, single, intravenous administration of a conjugate of the invention (SB-337), or (ii) the subsequent, triple, intratumoral administration of a vehicle (saline) or an immunostimulating polynucleotide.
  • FIG. 40 is a graph showing the survival rates (%) for Balb/c mice inoculated with A20 mouse lymphoma cells and subsequently treated with saline, free antibodies, antibody-immunostimulating polynucleotide conjugates, or free immunostimulating polynucleotides.
  • the control group are non-inoculated, untreated Balb/c mice.
  • the lines identified as CD22-10 and CD22-3 provide mouse survival rates (%) for the treatment regimens: 10 mg/kg of the free anti-mouse CD22 antibody and 3 mg/kg of the free anti-mouse CD22 antibody, respectively.
  • the lines identified as SB-337-10 and SB-337-3 provide mouse survival rates (%) for the treatment regimens: 10 mg/kg of SB-337 and 3 mg/kg of SB-337, respectively.
  • FIG. 41A is an image of a denaturing gel of samples of polynucleotides incubated in mouse serum at 37° C. for up to 24 hours.
  • FIG. 41B is an image of a denaturing gel of samples of polynucleotides incubated in mouse serum at 37° C. for up to 24 hours.
  • FIG. 41C is an image of a denaturing gel of samples of polynucleotides incubated in rat serum at 37° C. for up to 24 hours.
  • FIG. 41D is an image of a denaturing gel of samples of polynucleotides incubated in monkey serum at 37° C. for up to 24 hours.
  • FIG. 41E is an image of a denaturing gel of samples of polynucleotides incubated in human serum at 37° C. for up to 24 hours.
  • FIG. 42 is a graph showing the effect of phosphate-based and phosphorothioate-based internucleoside phosphodiesters at the 5′-terminus of an immunostimulating polynucleotide on the polynucleotide stability in 80% mouse serum.
  • FIG. 43 is a graph showing the proportions of degraded p246 and intact p246 in an aging experiment in 80% mouse serum.
  • FIG. 44 is a graph showing the effect of 5′-terminal nucleotide structures on the stability of the polynucleotides in 80% mouse serum.
  • FIG. 45 is a graph showing the effect of 5′-terminal nucleotide structures on the stability of the polynucleotides in 80% mouse serum, 80% non-human primate (NHP) serum, and 80% human serum.
  • the mouse serum data are marked with an asterisk, as these data were obtained in a separate study.
  • FIG. 46A illustrates the experimental scheme as described in Example 6, where mice having disseminated B-cell lymphoma were given intravenous doses of CpG-Ab (CpG ODN conjugated to a mouse anti-CD22 mAb).
  • FIG. 46B shows the survival rate of mice having disseminated B-cell lymphoma that were treated on Days 1, 3 and 5 with (i) 3 mg/kg CpG (p313)-mAb (CD22) conjugate (closed diamond); (ii) 10 mg/kg CpG-mAb (CD22) (closed triangle); (iii) naked CpG ODN (open triangle); (iv) 10 mg/kg CD22 mAb (closed square); (v) 10 mg/kg GpC-mAb control conjugate (open square); or (vi) saline solution (closed circle).
  • FIG. 46C shows the survival rates of mice which survived from the first tumor challenge and subsequently subjected to a second tumor challenge on Day 47. No treatment was given to the survivor after the second tumor challenge. Survivors treated with 10 mg/kg CpG-mAb (CD22) on Days 1, 3, and 5 (down triangle); survivors treated with 3 mg/kg CpG-mAb (CD22) on Days 1, 3, and 5 (diamond); second control group challenged with tumor cells on Day 47 and treated with saline solution (up triangle).
  • FIG. 46D shows the experiment where mice survived from the first and second tumor challenges were subsequently subjected to a third tumor challenge on Day 90. No treatment was given to the survivors after the second or third tumor challenge.
  • a third control group was challenged with tumor cells on Day 90 and treated with saline solution. The tumor volumes of survivors (square) and the control group (circle) were monitored between Day 90 and Day 120.
  • FIG. 47A illustrates the experimental scheme as described in Example 7, where mice having solid B-cell lymphoma were given intravenous doses of CpG-Ab (CpG ODN conjugated to a mouse anti-CD22 mAb).
  • FIG. 47B shows the tumor volume of mice having solid B-cell lymphoma that were treated on Day 9, 12 and 14 with (i) 3 mg/kg CpG-mAb (CD22) (open diamond); (ii) 10 mg/kg CpG-mAb (CD22) (large closed triangle); (iii) naked CpG ODN (open triangle); (iv) 10 mg/kg CD22 mAb (closed square); (v) 10 mg/kg GpC-mAb control conjugate (small closed square), or (vi) saline solution (closed circle).
  • FIG. 47C shows the tumor volume of mice having solid B-cell lymphoma that were treated with SB-337 DAR1 at 10 mg/kg or SB-337 DAR2 at 10 mg/kg in comparison with controls (saline and SB-339).
  • FIG. 47D shows the tumor volume of mice having solid B-cell lymphoma that were treated with SB-337 PEG24Bis DAR1 at 10 mg/kg or SB-337 PEG24Bis DAR2 at 10 mg/kg in comparison with controls (saline and SB-339).
  • FIG. 47E shows the tumor volume of mice having solid B-cell lymphoma that were treated with PD-1 at 10 mg/kg, PD-1 at 10 mg/kg plus SB-337 DAR1 at 3 mg/kg; or PD-1 at 10 mg/kg plus SB-337 DAR2 at 3 mg/kg in comparison with a saline control.
  • FIG. 47F shows the effect of p347, SB-337 DAR1, and SB-337 DAR2 on the weights of mice in comparison with controls (saline and mCD22).
  • FIG. 48A illustrates the experimental scheme as described in Example 8, where mice having solid colon carcinoma were given intravenous doses of B-cell targeting CpG-Ab (CpG ODN conjugated to a mouse anti-CD22 mAb) alone or in combination with anti-PD-1 antibody.
  • CpG-Ab CpG ODN conjugated to a mouse anti-CD22 mAb
  • FIG. 48B shows the tumor volume of mice having solid B-cell lymphoma model after receiving (i) 3 mg/kg CpG-mAb (CD22) (up triangle); (ii) anti-PD-1 antibody (closed square); (iii) 3 mg/kg CpG-mAb (CD22) in combination with anti-PD-1 antibody (down triangle); and (iv) saline solution (closed circle).
  • FIG. 49A shows the tumor volume in immune-competent Balb/C mice having solid B-cell lymphoma after receiving (i) 10 mg/kg CpG-mAb (CD22) (triangle) or saline solution (circle).
  • FIG. 49B shows the tumor volume in immune-compromised Nu/Nu mice having solid B-cell lymphoma after receiving (i) 10 mg/kg CpG-mAb (CD22) (square), (ii) naked CpG ODN (triangle) or (iii) saline solution (circle).
  • FIG. 49C shows the tumor volume in immune-compromised SCID mice having solid B-cell lymphoma after receiving (i) 10 mg/kg CpG-mAb (CD22) (square), (ii) naked CpG ODN (triangle) or (iii) saline solution (circle).
  • FIG. 50A shows the survival rate of mice having soluble B-cell lymphoma after receiving (i) CpG-mAb (CD22) alone (open circle); (ii) CpG-mAb (CD22) and CD4+ T cell depletion treatment (open square); (iii) CD4+ T cell depletion treatment (closed square); or (iv) saline solution (closed circle).
  • FIG. 50B shows the survival rate of mice having soluble B-cell lymphoma after receiving (i) CpG-mAb (CD22) alone (open circle); (ii) CpG-mAb (CD22) and nature killer (NK) cell depletion treatment (open square); (iii) NK cell depletion treatment (closed square); or (iv) saline solution (closed circle).
  • FIG. 50C shows the survival rate of mice having soluble B-cell lymphoma after receiving (i) CpG-mAb (CD22) alone (open circle); (ii) CpG-mAb (CD22) and CD8+ T cell depletion treatment (open square); (iii) CD8+ T cell depletion treatment (closed square); or (iv) saline solution (closed circle).
  • FIG. 51A shows the tumor volume in mice having solid B-cell lymphoma after receiving CpG-mAb (CD22) (square) or saline solution (circle). Mice were sacrificed and tumor were harvested on Day 17 for digestion.
  • FIG. 51B shows the percentage of CD4+ or CD8+ live gate cells in tumors harvested from mice having solid B-cell lymphoma treated with (i) CpG-Ab (square) or (ii) saline solution (circle).
  • FIG. 51C shows the correlation between the percentage of CD8+ tumor cells and the tumor volume in mice treated with (i) CpG-Ab (square) or (ii) saline solution (circle).
  • FIG. 52A shows the tumor volume in mice having solid B-cell lymphoma after receiving (i) CpG-mAb (CD22) alone (open circle); (ii) anti-PD-1 antibody alone (closed square); (iii) CpG-mAb (CD22) in combination with anti-PD-1 antibody (open square); or (iv) saline solution (closed circle).
  • FIG. 52B shows the tumor volume in mice having solid B-cell lymphoma after receiving (i) CpG-mAb (CD22) alone (open circle); (ii) anti-PD-L1 antibody alone (closed triangle); (iii) CpG-mAb (CD22) in combination with anti-PD-L1 antibody (open triangle); or (iv) saline solution (closed circle).
  • FIG. 52C shows the tumor volume in mice having solid B-cell lymphoma after receiving (i) CpG-mAb (CD22) alone (open circle); (ii) anti-PD-1 antibody alone (closed square); (iii) CpG-mAb (CD22) in combination with anti-PD-1 antibody (open square); (iv) CpG-mAb (CD22) in combination with anti-PD-1 antibody and CD8+ T cell depletion treatment; or (v) saline solution (closed circle).
  • FIG. 53A shows the average tumor volume in mice having solid B-cell lymphoma after receiving (i) anti-PD-1 antibody alone (square); (ii) CpG-mAb (CD22) in combination with anti-PD-1 antibody (diamond); or (iii) saline solution (circle).
  • FIG. 53B shows the tumor volumes in individual mice having solid B-cell lymphoma after receiving anti-PD-1 antibody alone.
  • FIG. 53C shows the tumor volumes in individual mice having solid B-cell lymphoma after receiving the CpG-mAb (CD22)/anti-PD-1 antibody combination treatment.
  • FIG. 53D shows the tumor volume of survivors from the first tumor challenge (up triangle) and a naive control group (down triangle) after the second tumor challenge.
  • FIG. 54A shows the tumor volume in mice having solid B-cell lymphoma after receiving (i) (i) anti-OX40 antibody alone (triangle); (ii) CpG-mAb (CD22) in combination with anti-OX40 antibody (diamond); or (iii) saline solution (circle).
  • FIG. 54B shows the tumor volume in mice having solid B-cell lymphoma after receiving (i) (i) anti-ICOS antibody alone (square); (ii) CpG-mAb (CD22) in combination with anti-ICOS antibody (triangle); or (iii) saline solution (circle).
  • FIG. 54C shows the tumor volume in mice having solid B-cell lymphoma after receiving (i) anti-4-1 BB antibody alone (diamond); (ii) CpG-mAb (CD22) in combination with anti-4-1 BB antibody (triangle); or (iii) saline solution (circle).
  • FIG. 55A shows the tumor volume in mice having colon carcinoma after receiving (i) 10 mg/kg CpG-mAb (CD22) or (i) saline solution on each of Days 10, 13 and 16.
  • FIG. 55B shows the number of IFN-gamma secreting cells in 10 6 splenocytes isolated from mice treated with (i) CpG-mAb (CD22) or (i) saline solution, before or after stimulating the cells with the AH1 antigen.
  • FIG. 56A shows the average tumor volume in mice having solid B-cell lymphoma after receiving intravenous doses of (i) 10 mg/kg CpG-Ab (PD-L1) (diamond); (i) 10 mg/kg CpG-Ab (CD205) (triangle); or (iii) saline solution on each of Days 10, 12 and 14.
  • FIG. 56B shows the tumor volumes in individual mice having B-cell lymphoma after receiving intravenous doses of 10 mg/kg CpG-Ab (CD205) on Days 10, 12, and 14.
  • FIG. 56C shows the tumor volumes in individual mice having B-cell lymphoma after receiving intravenous doses of 10 mg/kg CpG-Ab (PD-L1) on Days 10, 12, and 14.
  • FIG. 56D shows the tumor volume of survivors from the first tumor challenge which were treated with CpG-Ab (CD205) (square) or treated with CpG-Ab (PD-L1) (triangle) and a na ⁇ ve control group (circle) after the second tumor challenge given at Day 38.
  • FIG. 57A shows the average tumor volume in mice having solid B-cell lymphoma after receiving intravenous doses of (i) 10 mg/kg CpG-Ab (CD205) (triangle); (ii) 10 mg/kg anti-CD205 antibody (square); (iii) 10 mg/kg mouse IgG (open circle); or (iv) saline solution (closed circle), on each of Days 10, 12 and 14.
  • FIG. 57B shows the tumor volumes in individual mice having solid B-cell lymphoma after receiving intravenous doses of 10 mg/kg anti-CD205 antibody on each of Days 10, 12 and 14.
  • FIG. 57C shows the tumor volumes in individual mice having solid B-cell lymphoma after receiving intravenous doses of 10 mg/kg CpG-Ab (CD205) on each of Days 10, 12 and 14.
  • FIG. 57D shows the tumor volumes in individual mice having solid B-cell lymphoma after receiving intravenous doses of 10 mg/kg rat IgG2a antibody on each of Days 10, 12 and 14.
  • FIG. 58 shows NF ⁇ B activation in human Ramos cells after treated with anti-CD38 antibody conjugated to p246 (closed squares), with anti-CD38 antibody conjugated to p4 (closed circles), with unconjugated p246 (open squares) or with unconjugated p4 (open circles).
  • FIG. 59 shows complement activation (as measured by C3 release) after incubating monkey serum with Zymosan (inverted triangle; positive control), p1 (closed circles), or two CpG-containing immunostimulating polynucleotides as provided herein (closed squares and closed triangles).
  • FIG. 60A shows the average tumor volume growth progression of mice with A20 mouse B-cell lymphoma cell xenografts following intravenous doses of (i) saline solution (closed circle); (ii) 3 mg/kg CpG-Ab (4523-CD22; SB-337) (square); (Hi) 3 mg/kg CD19-mAb (down closed triangle); (iv) 3 mg/kg CpG-Ab (4523-CD19; SB-388) (closed diamond); (v) 1.9 ⁇ g/mouse naked CpG (P347) (up triangle); (vi) 19 ⁇ g/mouse naked CpG (p347) (down open triangle); (vii) 190 ⁇ g/mouse naked CpG (P347) (open diamond); on each of Days 10, 12 and 14.
  • FIG. 60B shows the average tumor volume at Day 20 of mice with A20 mouse B-cell lymphoma cell xenografts following intravenous doses of (i) saline solution (solid); (ii) 3 mg/kg CpG-Ab (SB-337) (checkered); (iii) 3 mg/kg CD19-mAb (horizontal); (iv) 3 mg/kg CpG-Ab (SB-388) (vertical); (v) 1.9 ⁇ g/mouse naked CpG (P347) (downward diagonal); on each of Days 10, 12 and 14.
  • FIG. 60C shows the average body weight change with the tumor weight change removed at Day 20 of mice with A20 mouse B-cell lymphoma cell xenografts following intravenous doses of (i) saline solution (filled); (ii) 3 mg/kg CpG-Ab (SB-337) (checkered); (iii) 3 mg/kg CD19-mAb (horizontal); (iv) 3 mg/kg CpG-Ab (SB-388) (vertical); (v) 1.9 ⁇ g/mouse naked CpG (P347) (downward diagonal); (vi) 19 ⁇ g/mouse naked CpG (P347) (grid); (vii) 190 ⁇ g/mouse naked CpG (P347) (upward diagonal); on each of Days 10, 12 and 14.
  • FIG. 61A shows the average tumor volume growth progression of mice after B16F10 melanoma re-challenge following intratumoral dosing of (i) saline solution (closed circle); or (ii) p347 (closed square); on each of Days 7, 9, 11, and 13, and re-challenge on day 14.
  • FIG. 61B shows the lung metastases from mice after B16F10 melanoma re-challenge following intratumoral dosing of saline solution (top panel), or p347 (bottom panel); on each of Days 7, 9, 11, and 13, and re-challenge on day 14.
  • FIG. 61C shows the average tumor volume growth progression of mice inoculated with CT26 colorectal xenografts following intratumoral dosing of (i) saline solution (upward triangle); or (ii) p347 (downward triangle); on each of Days 7, 10, 12, and 14.
  • FIG. 62A shows the average tumor volume growth progression of genetic B-cell deficient mice using CT26 colorectal model following intravenous dosing of (i) saline solution (circle); or (ii) 10 mg/kg CpG-mAb (SB-337) (square); on each of Days 10, 12, and 14.
  • FIG. 62B shows the average tumor volume growth progression of anti-CD20 mAb B-cell depleted mice using CT26 colorectal model following intravenous dosing of (i) saline solution (circle); or (ii) 10 mg/kg CpG-mAb (SB-337) (square); on each of Days 10, 12, and 14.
  • FIG. 63A shows the average tumor volume growth progression of mice using a MC38 colorectal syngeneic model following dosing of (i) saline solution (circle); (ii) 10 mg/kg anti-CD22 (upward triangle); (iii) 10 mg/kg anti-PD-L1 (downward triangle); (iv) 10 mg/kg CD22-CpG (SB-337) (square); or (v) 10 mg/kg CD22-CpG (SB-337)+10 mg/kg anti-PD-L1 (diamond).
  • FIG. 63B shows the tumor volume growth progression of each mouse using a MC38 colorectal syngeneic model following intravenous dosing saline on Days 10, 12, and 14
  • FIG. 63C shows the tumor volume growth progression of each mouse using a MC38 colorectal syngeneic model following intravenous dosing of 10 mg/kg of anti-CD22 mAb on Days 10, 12, and 14.
  • FIG. 63D shows the tumor volume growth progression of each mouse using a MC38 colorectal syngeneic model following intraperitoneal dosing of 10 mg/kg of anti-PD-L1 on Days 10, 13, and 17.
  • FIG. 63E shows the tumor volume growth progression of each mouse using a MC38 colorectal syngeneic model following intravenous dosing of 10 mg/kg of CD22-CpG (SB-337) on Days 10, 12, and 14.
  • FIG. 63F shows the tumor volume growth progression of each mouse using a MC38 colorectal syngeneic model following intravenous dosing of 10 mg/kg of CD22-CpG (SB-337) on Days 10, 12, and 14, plus intraperitoneal dosing of 10 mg/kg of anti-PD-L1 on Days 10, 13, and 17.
  • FIG. 64A shows the average tumor volume growth progression of mice using a B16F10 melanoma model following dosing of (i) saline solution (circle); (ii) 10 mg/kg anti-CD22 (square); (iii) 10 mg/kg CD22-CpG (SB-337) (triangle); or (iv) 10 mg/kg CD22-CpG (SB-337)+10 mg/kg anti-PD-L1 (diamond) on Days 10, 12, and 14.
  • FIG. 64B shows the average tumor volume growth progression of mice using a LLC1 Lewis lung carcinoma model following dosing of (i) saline solution (circle); (ii) 10 mg/kg CD22-CpG (SB-337) (circle); (iii) 10 mg/kg anti-PD1 (square); (iv) 10 mg/kg CD22-CpG (SB-337)+10 mg/kg anti-PD1 (upward triangle) (v) 10 mg/kg anti-PD-L1 (downward triangle); (vi) 10 mg/kg CD22-CpG+10 mg/kg anti-PD-L1 (diamond).
  • FIG. 65A shows the average tumor volume growth progression of mice using the CT26 colorectal model following intravenous dosing of (i) saline solution (circle); (ii) 10 mg/kg CD22-CpG (SB-337) (triangle); or (iii) 10 mg/kg DEC205-CpG (SB-3096) on each of Days 12, 17, 20, and 24.
  • FIG. 65B shows the tumor volume growth progression of each mouse using the CT26 colorectal model following intravenous dosing of saline on each of Days 12, 17, 20, and 24.
  • FIG. 65C shows the tumor volume growth progression of each mouse using the CT26 colorectal model following intravenous dosing of 10 mg/kg CD22-CpG (SB-337) on each of Days 12, 17, 20, and 24.
  • FIG. 65D shows the tumor volume growth progression of each mouse using the CT26 colorectal model following intravenous dosing of 10 mg/kg DEC205-CpG (SB-3096) on each of Days 12, 17, 20, and 24.
  • FIG. 66A shows the average tumor volume growth progression of mice using a CT26 colorectal model following dosing of (i) saline solution (small circle); (ii) CD4 depletion (big circle); (iii) 3 mg/kg CD22-CpG (SB-337) (square); or (iv) CD4 depletion+3 mg/kg CD22-CpG (SB-337) (diamond).
  • CD22-CpG was dosed intravenously on Days 10, 13; and 15. CD4 depletion was performed using anti-CD4.
  • FIG. 66B shows the average tumor volume growth progression of mice using an A20 lymphoma model following dosing of (i) saline solution (circle); (ii) CD4 depletion (upward triangle); (iii) 3 mg/kg CD22-CpG (SB-337) (square); or (iv) CD4 depletion+3 mg/kg CD22-CpG (SB-337) (downward triangle).
  • CD22-CpG was dosed intravenously on Days 10, 12; and 14. CD4 depletion was performed using anti-CD4
  • FIG. 67A shows the mean fluorescence intensity (MFI) of CD40, CD70, CD80, CD86, MHC-I, MHC II, and 4-1 BBL surface expression on CD19+/B220+ B-cells after in vitro incubation with 1 nM CD22 Ab (checkered); 1 nM CpG (SB-4715) (horizontal line); or 1 nM CpG-Ab (SB-337) (vertical line).
  • MFI mean fluorescence intensity
  • FIG. 67B shows the mean fluorescence intensity (MFI) of CD40, CD80, CD86, and MHC II surface expression on CD19+/B220+ B-cells after in vivo dosing with saline (solid); 10 mg/kg CD22 Ab (checkered); 10 mg/kg CpG (SB-4715) (horizontal line); or 10 mg/kg CpG-Ab (SB-337) (vertical line).
  • MFI mean fluorescence intensity
  • FIG. 68A shows the percent of activated T-cells (CD71+, CD3+) relative to total T-cell (CD3+) population in mice treated with (i) saline (solid); (ii) Ab (anti-CD22) (checkered); (iii) CpG-Ab (SB-337) (horizontal); or (iv) CpG (SB-4715) (vertical).
  • FIG. 68B shows the percent of activated T-cells (Ki67+, CD3+) relative to total T-cell (CD3+) population in mice treated with (i) saline (solid); (ii) Ab (anti-CD22) (checkered); (iii) CpG-Ab (SB-337) (horizontal); or (iv) CpG (SB-4715) (vertical).
  • FIG. 69A shows the average tumor volume growth progression of mice using the CT26 colorectal model following intravenous dosing of (i) saline solution (circle); (ii) 10 mg/kg CD22-CpG (SB-337) (square); (iii) 10 mg/kg CD22 (upward triangle); or (iv) Free CpG (P347) (downward triangle) on each of Days 10, 12, 14.
  • FIG. 69B shows the average tumor volume growth progression of mice using the CT26 colorectal model following adoptively transferred draining lymph node cells from mice treated with (i) saline solution (small circle); (ii) 10 mg/kg CD22-CpG (SB-337) (small square); (iii) 10 mg/kg CD22 (small upward triangle); or (iv) Free CpG (P347) (small downward triangle); or non-draining lymph node cells from mice treated with (v) saline solution (diamond); (vi) 10 mg/kg CD22-CpG (SB-337) (large circle); (vii) 10 mg/kg CD22 (large square); or (viii) Free CpG (P347) (large upward triangle).
  • FIG. 69C shows the average tumor volume on Day 24 for mice using the CT26 colorectal model following adoptively transferred draining lymph node cells from mice treated with (i) saline solution (upward narrow diagonal); (ii) 10 mg/kg CD22-CpG (SB-337) (downward narrow diagonal); (iii) 10 mg/kg CD22 (grid); or (iv) Free CpG (P347) (wide downward diagonal); or non-draining lymph node cells from mice treated with (v) saline solution (solid); (vi) 10 mg/kg CD22-CpG (SB-337) (checkered); (vii) 10 mg/kg CD22 (horizontal); or (viii) Free CpG (P347) (empty).
  • FIG. 70A shows the plasma concentration of IL-6 in na ⁇ ve mice treated intravenously with (i) saline (solid); (ii) 10 mg/kg Ab (CD22) (checkered); (iii) 5.7 ug/dose free CpG (p347) (horizontal); or (iv) 10 mg/kg CpG-mAb (SB-337) (vertical).
  • FIG. 70B shows the plasma concentration of IL-1 ⁇ in na ⁇ ve mice treated intravenously with (i) saline (solid); (ii) 10 mg/kg Ab (CD22) (checkered); (iii) 5.7 ug/dose free CpG (p347) (horizontal); or (iv) 10 mg/kg CpG-mAb (SB-337) (vertical).
  • FIG. 70C shows the plasma concentration of IL-10 in na ⁇ ve mice treated intravenously with (i) saline (solid); (ii) 10 mg/kg Ab (CD22) (checkered); (iii) 5.7 ug/dose free CpG (p347) (horizontal); or (iv) 10 mg/kg CpG-mAb (SB-337) (vertical).
  • FIG. 70D shows the plasma concentration of IL-12p70 in na ⁇ ve mice treated intravenously with (i) saline (solid); (ii) 10 mg/kg Ab (CD22) (checkered); (iii) 5.7 ug/dose free CpG (Sp347) (horizontal); or (iv) 10 mg/kg CpG-mAb (SB-337) (vertical).
  • FIG. 70E shows the plasma concentration of IFN ⁇ in na ⁇ ve mice treated intravenously with (i) saline (solid); (ii) 10 mg/kg Ab (CD22) (checkered); (iii) 5.7 ug/dose free CpG (p347) (horizontal); or (iv) 10 mg/kg CpG-mAb (SB-337) (vertical).
  • FIG. 70F shows the plasma concentration of TNF ⁇ in na ⁇ ve mice treated intravenously with (i) saline (solid); (ii) 10 mg/kg Ab (CD22) (checkered); (iii) 5.7 ug/dose free CpG (p347) (horizontal); or (iv) 10 mg/kg CpG-mAb (SB-337) (vertical).
  • FIG. 71A shows the percentage of B-cells (B220+) relative to total cell in spleen from mice using the CT26 colorectal model following intravenous dosing of (i) saline (circle); or (ii) 10 mg/kg CpG-mAb (SB-337) (square) on each of Days 10, 13, and 17. * p ⁇ 0.05
  • FIG. 71B shows the percentage of germinal center (GC) cells (B220 + , IgD lo , Fas + ) relative to total cell in spleen from mice using the CT26 colorectal model following intravenous dosing of (i) saline (circle); or (ii) 10 mg/kg CpG-mAb (SB-337) (square) on each of Days 10, 13, and 17. * p ⁇ 0.05
  • FIG. 71C shows the percentage of T follicular helper (T fh ) cells (CD4 + , CXCR5 + , PD-1 + ) relative to total cell in spleen from mice using the CT26 colorectal model following intravenous dosing of (i) saline (circle); or (ii) 10 mg/kg CpG-mAb (SB-337) (square) on each of Days 10, 13, and 17. * p ⁇ 0.05
  • FIG. 71D shows the relative fold change of IL-21 from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 10 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17. *p ⁇ 0.05
  • FIG. 71E shows the relative fold change of Bcl-6 from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 10 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17. *p ⁇ 0.05
  • FIG. 71F shows the relative fold change of IRF-4 from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 10 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17. *p ⁇ 0.05
  • FIG. 72A shows the relative fold change of IL-6 in the spleen from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17.
  • FIG. 72B shows the relative fold change of IL-10 in the spleen from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17.
  • FIG. 72C shows the relative fold change of IL-1 ⁇ in the spleen from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17.
  • FIG. 72D shows the relative fold change of TNF ⁇ in the spleen from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17.
  • FIG. 73A shows the relative fold change of IL-6 in the draining lymph node from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17.
  • FIG. 73B shows the relative fold change of IL-10 in the draining lymph node from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17.
  • FIG. 73C shows the relative fold change of IL-1 ⁇ in the draining lymph node from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17.
  • FIG. 73D shows the relative fold change of TNF ⁇ in the draining lymph node from mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 17.
  • FIG. 74A shows the concentration of IgM in mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 16. * p ⁇ 0.05.
  • FIG. 74B shows the concentration of IgG2a in mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 16. *p ⁇ 0.05
  • FIG. 74C shows the concentration of IgG in mice using the CT26 colorectal model following intravenous dosing of (i) saline; or (ii) 3 mg/kg CpG-mAb (SB-337) on each of Days 10, 13, and 16. * p ⁇ 0.05
  • FIG. 75 shows the scheme and quantification of mouse anti-AH1 IgG2a in the serum from mice treated intravenously with saline (circle), or 3 mg/kg of CpG-mAb (SB-337) (square) measured using a commercially available secondary anti-mouse IgG2a-HRP antibodies, 2 nd Ab1; or measuring treatment with saline (downward triangle), or 3 mg/kg of CpG-mAb (SB-337) (diamond) using a second commercially available secondary anti-mouse IgG2a-HRP antibodies, 2 nd Ab2.
  • FIG. 76A shows the percentage of regulatory B cells (Bregs; CD19 + , B220 + , CD1d hi ) relative to total B-cells (B220+) in spleen from mice following weekly intravenous dosing of (i) saline (circle); or (ii) 10 mg/kg CpG-mAb (SB-337) (square). * p ⁇ 0.001
  • FIG. 76B shows the percentage of regulatory B cells (Bregs; CD19 + , B220 + , CD1d hi ) relative to total cells in spleen from mice following weekly intravenous dosing of (i) saline (circle); or (ii) 10 mg/kg CpG-mAb (SB-337) (square). * p ⁇ 0.001
  • FIG. 77B shows the percentage of pooled lymph node (LN) myeloid dendritic cells (mDC; B220 ⁇ , CD11C + ; CD8 + ) relative to total cells from mice using the CT26 colorectal model treated intravenously with (i) saline (circle); (ii) 10 mg/kg CpG-mAb (SB-337) (square); or (iii) 10 mg/kg CpG (triangle); on each of Days 14, 17, and 30. Sample were taken from drained lymph nodes (dLN) and non-drained lymph nodes (ndLN).
  • LN pooled lymph node
  • mDC myeloid dendritic cells
  • FIG. 78A shows the average tumor volume growth progression of mice using the CT26 colorectal model following treatment with (i) saline solution (circle); (ii) plasmacytoid dendritic cell (pDC) depletion (downward triangle); (iii) 3 mg/kg CD22-CpG (SB-337) (square); or (iv) pDC depletion+3 mg/kg CD22-CpG (SB-337) (upward triangle) on each of Days 10, 13, and 15.
  • saline solution circle
  • pDC plasmacytoid dendritic cell
  • FIG. 78B shows the average tumor volume growth progression of mice using the A20 lymphoma model following treatment with (i) saline solution (small circle); (ii) plasmacytoid dendritic cell (pDC) depletion (diamond); (iii) 3 mg/kg CD22-CpG (SB-337) (square); or (iv) pDC depletion+3 mg/kg CD22-CpG (SB-337) (large circle) on each of Days 10, 12, and 14.
  • saline solution small circle
  • pDC plasmacytoid dendritic cell
  • FIG. 79A shows the relative fold change in gene expression of T-cell genes from mice using the CT26 colorectal model following intravenous dosing of (i) saline (solid); or (ii) 3 mg/kg CpG-mAb (SB-337) (checkered) on each of Days 10, 12, and 14.
  • FIG. 79B shows the relative fold change in gene expression of macrophage genes from mice using the CT26 colorectal model following intravenous dosing of (i) saline (solid); or (ii) 3 mg/kg CpG-mAb (SB-337) (horizontal) on each of Days 10, 12, and 14.
  • FIG. 79C shows the relative fold change in gene expression of cytokine genes from mice using the CT26 colorectal model following intravenous dosing of (i) saline (solid); or (ii) 3 mg/kg CpG-mAb (SB-337) (vertical) on each of Days 10, 12, and 14.
  • FIG. 79D shows the relative fold change in gene expression of apoptotic enzyme genes from mice using the CT26 colorectal model following intravenous dosing of (i) saline (solid); (ii) 3 mg/kg CpG-mAb (SB-337) (upward diagonal); (iii) anti-PD-L1 (downward diagonal); (iv) 3 mg/kg CpG-mAb+anti-PD-L1 (SB-337) (grid) on each of Days 10, 12, and 14.
  • FIG. 80A shows a dose response curve for the concentration of IL-6 from human primary B-cells in response to in vitro treatment with (i) CpG (p425) (square); (ii) CpG-Ab (SB-430) (triangle); or (iii) Ab (diamond) for 24-72 hours.
  • FIG. 80B shows a dose response curve for the mean fluorescence intensity (MFI) of MHC II expression on human primary B-cells in response to in vitro treatment with (i) CpG (p425) (triangle); or (ii) CpG-Ab (SB-430) (circle) for 24-72 hours.
  • MFI mean fluorescence intensity
  • FIG. 80C shows a dose response curve for the mean fluorescence intensity (MFI) of CD86 expression on human primary B-cells in response to in vitro treatment with (i) CpG (p425) (triangle); or (ii) CpG-Ab (SB-430) (circle) for 24-72 hours.
  • MFI mean fluorescence intensity
  • FIG. 80D shows a dose response curve for the mean fluorescence intensity (MFI) of CD70 expression on human primary B-cells in response to in vitro treatment with (i) CpG (p425) (triangle); or (ii) CpG-Ab (SB-430) (circle) for 24-72 hours.
  • MFI mean fluorescence intensity
  • FIG. 80E shows a dose response curve for the mean fluorescence intensity (MFI) of CD20 expression on human primary B-cells in response to in vitro treatment with (i) CpG (p425) (triangle); or (ii) CpG-Ab (SB-430) (circle) for 24-72 hours.
  • MFI mean fluorescence intensity
  • FIG. 81 shows a dose response curve for the concentration of IL-6 from primary human splenocytes in response to in vitro treatment with (i) hCD22-hCpG (SB-430) (square); (ii) Free human CpG 7909 (downward triangle); or (iii) Free human CpG Solstice (p425) (upward arrow) for 24 hours
  • FIG. 82A shows the scheme for the humanized mouse model experiment using intraperitoneally (IP) injected fresh human peripheral blood mononuclear cells (hPBMC) prior to subcutaneous transplantation of Daudi Burkitt lymphoma cells and intravenous (IV) treatment at each of Days 12, 14, and 16.
  • IP intraperitoneally
  • hPBMC fresh human peripheral blood mononuclear cells
  • IV intravenous
  • FIG. 82B shows the average tumor volume growth progression in a humanized mouse model intraperitoneally injected with fresh human peripheral blood mononuclear cells prior to subcutaneous transplantation of Daudi Burkitt lymphoma cells and intravenous (IV) treatment with (i) saline (circle); (ii) 5 mg/kg hCD22 Ab (square); (iii) 5.7 ⁇ g/dose CpG (p425) (open triangle); or (iv) 5 mg/kg hCD22-CpG (SB-430) (closed triangle), at each of Days 12, 14, and 16.
  • IV intravenous
  • FIG. 83 shows pharmacokinetic profiles of CpG-antibody conjugate SB-337 DAR1 in mice administered intravenously or subcutaneously.
  • FIG. 84 shows pharmacokinetic profiles of CpG-antibody conjugate SB-337 DAR1 in mice administered intravenously.
  • FIG. 85 shows pharmacokinetic profiles of CpG-antibody conjugate SB-337 DAR1 in mice administered intravenously.
  • FIG. 86 shows pharmacokinetic profiles of CpG-antibody conjugates SB-337 DAR1 and SB-337 DAR2 in mice administered intravenously.
  • FIGS. 87A and 87B show pharmacokinetic profiles of CpG-antibody conjugates in mice administered intravenously.
  • abasic spacer represents a divalent group of the following structure: R 1 -L 1 -[-L 2 -(L 1 ) n1 -] n2 -R 2 , (I) wherein:
  • n1 0 or 1
  • n2 is an integer from 1 to 6
  • R 1 is a bond to a nucleoside in the immunomodulating polynucleotide
  • R 2 is a bond to a nucleoside in the immunomodulating polynucleotide or to a capping group
  • each L 1 is independently a phosphodiester or a phosphotriester
  • each L 2 is a sugar analogue
  • alkane-tetrayl represents a tetravalent, acyclic, straight or branched chain, saturated hydrocarbon group having from 1 to 16 carbons, unless otherwise specified. Alkane-tetrayl may be optionally substituted as described for alkyl.
  • alkane-triyl represents a trivalent, acyclic, straight or branched chain, saturated hydrocarbon group having from 1 to 16 carbons, unless otherwise specified. Alkane-triyl may be optionally substituted as described for alkyl.
  • alkanoyl represents hydrogen or an alkyl group that is attached to the parent molecular group through a carbonyl group and is exemplified by formyl (i.e., a carboxyaldehyde group), acetyl, propionyl, butyryl, and iso-butyryl.
  • Unsubstituted alkanoyl groups contain from 1 to 7 carbons.
  • the alkanoyl group may be unsubstituted of substituted (e.g., optionally substituted C 1-7 alkanoyl) as described herein for alkyl group.
  • the ending “-oyl” may be added to another group defined herein, e.g., aryl, cycloalkyl, and heterocyclyl, to define “aryloyl,” “cycloalkanoyl,” and “(heterocyclyl)oyl.” These groups represent a carbonyl group attached to aryl, cycloalkyl, or heterocyclyl, respectively.
  • aryloyl cycloalkanoyl
  • (heterocyclyl)oyl may be optionally substituted as defined for “aryl,” “cycloalkyl,” or “heterocyclyl,” respectively.
  • alkenyl represents acyclic monovalent straight or branched chain hydrocarbon groups of containing one, two, or three carbon-carbon double bonds.
  • alkenyl groups include ethenyl, prop-1-enyl, prop-2-enyl, 1-methylethenyl, but-1-enyl, but-2-enyl, but-3-enyl, 1-methylprop-1-enyl, 2-methylprop-1-enyl, and 1-methylprop-2-enyl.
  • Alkenyl groups may be optionally substituted as defined herein for alkyl.
  • alkenylene refers to a straight or branched chain alkenyl group with one hydrogen removed, thereby rendering this group divalent.
  • alkenylene groups include ethen-1,1-diyl; ethen-1,2-diyl; prop-1-en-1,1-diyl, prop-2-en-1,1-diyl; prop-1-en-1,2-diyl, prop-1-en-1,3-diyl; prop-2-en-1,1-diyl; prop-2-en-1,2-diyl; but-1-en-1,1-diyl; but-1-en-1,2-diyl; but-1-en-1,3-diyl; but-1-en-1,4-diyl; but-2-en-1,1-diyl; but-2-en-1,2-diyl; but-2-en-1,3-diyl; but-2-en-1,4-diyl; but-2-en-1,1-di
  • alkoxy represents a chemical substituent of formula —OR, where R is a C 1-6 alkyl group, unless otherwise specified. In some embodiments, the alkyl group can be further substituted as defined herein.
  • alkoxy can be combined with other terms defined herein, e.g., aryl, cycloalkyl, or heterocyclyl, to define an “aryl alkoxy,” “cycloalkyl alkoxy,” and “(heterocyclyl)alkoxy” groups. These groups represent an alkoxy that is substituted by aryl, cycloalkyl, or heterocyclyl, respectively.
  • aryl alkoxy,” “cycloalkyl alkoxy,” and “(heterocyclyl)alkoxy” may optionally substituted as defined herein for each individual portion.
  • alkyl refers to an acyclic straight or branched chain saturated hydrocarbon group, which, when unsubstituted, has from 1 to 12 carbons, unless otherwise specified. In certain preferred embodiments, unsubstituted alkyl has from 1 to 6 carbons.
  • Alkyl groups are exemplified by methyl; ethyl; n- and iso-propyl; n-, sec-, iso- and tert-butyl; neopentyl, and the like, and may be optionally substituted, valency permitting, with one, two, three, or, in the case of alkyl groups of two carbons or more, four or more substituents independently selected from the group consisting of: amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; cycloalkenyl; cycloalkynyl; halo; heterocyclyl; (heterocyclyl)oxy; hydroxy; nitro; thiol; silyl; cyano; ⁇ O; ⁇ S; ⁇ NR′, where R′ is H, alkyl, aryl, or heterocyclyl.
  • Each of the substituents may itself be unsubstituted or, valency permitting
  • alkylamino refers to a group having the formula —N(R N1 ) 2 or —NHR N1 , in which R N1 is alkyl, as defined herein.
  • the alkyl portion of alkylamino can be optionally substituted as defined for alkyl.
  • Each optional substituent on the substituted alkylamino may itself be unsubstituted or, valency permitting, substituted with unsubstituted substituent(s) defined herein for each respective group.
  • alkyl cycloalkylene refers to a saturated divalent hydrocarbon group that is an alkyl cycloalkane, in which two valencies replace two hydrogen atoms. Preferably, at least one of the two valencies is present on the cycloalkane portion.
  • the alkane and cycloalkane portions may be optionally substituted as the individual groups as described herein.
  • alkylene refers to a saturated divalent hydrocarbon group that is a straight or branched chain saturated hydrocarbon, in which two valencies replace two hydrogen atoms.
  • the valency of alkylene defined herein does not include the optional substituents.
  • Non-limiting examples of the alkylene group include methylene, ethane-1,2-diyl, ethane-1,1-diyl, propane-1,3-diyl, propane-1,2-diyl, propane-1,1-diyl, propane-2,2-diyl, butane-1,4-diyl, butane-1,3-diyl, butane-1,2-diyl, butane-1,1-diyl, and butane-2,2-diyl, butane-2,3-diyl.
  • C x-y alkylene represents alkylene groups having between x and y carbons. Exemplary values for x are 1, 2, 3, 4, 5, and 6, and exemplary values for y are 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12. Alkylene can be optionally substituted as described herein for alkyl.
  • alkylsulfenyl represents a group of formula —S-(alkyl). Alkylsulfenyl may be optionally substituted as defined for alkyl.
  • alkylsulfinyl represents a group of formula —S(O)-(alkyl). Alkylsulfinyl may be optionally substituted as defined for alkyl.
  • alkylsulfonyl represents a group of formula —S(O) 2 -(alkyl). Alkylsulfonyl may be optionally substituted as defined for alkyl.
  • alkynyl represents monovalent straight or branched chain hydrocarbon groups of from two to six carbon atoms containing at least one carbon-carbon triple bond and is exemplified by ethynyl, 1-propynyl, and the like.
  • the alkynyl groups may be unsubstituted or substituted (e.g., optionally substituted alkynyl) as defined for alkyl.
  • 5-alkynyluridine represents a nucleoside, in which the nucleobase is 5-alkynyluracil of the following structure:
  • R is a bond to the anomeric carbon of the pentafuranose of the nucleoside
  • X is alkynyl.
  • X is ethynyl or propynyl (e.g., X is ethynyl).
  • alkynylene refers to a straight-chain or branched-chain divalent substituent including one or two carbon-carbon triple bonds and containing only C and H when unsubstituted.
  • alkynylene groups include ethyn-1,2-diyl; prop-1-yn-1,3-diyl; prop-2-yn-1,1-diyl; but-1-yn-1,3-diyl; but-1-yn-1,4-diyl; but-2-yn-1,1-diyl; but-2-yn-1,4-diyl; but-3-yn-1,1-diyl; but-3-yn-1,2-diyl; but-3-yn-2,2-diyl; and buta-1,3-diyn-1,4-diyl.
  • the alkynylene group may be unsubstituted or substituted (e.g., optionally substituted al
  • amino represents —N(R N1 ) 2 , where, if amino is unsubstituted, both R N1 are H; or, if amino is substituted, each R N1 is independently H, —OH, —NO 2 , —N(R N2 ) 2 , —SO 2 OR N2 , —SO 2 R N2 , —SOR N2 , —COOR N2 , an N-protecting group, alkyl, alkenyl, alkynyl, alkoxy, aryl, arylalkyl, aryloxy, cycloalkyl, cycloalkenyl, heteroalkyl, or heterocyclyl, provided that at least one R N1 is not H, and where each R N2 is independently H, alkyl, or aryl.
  • amino is unsubstituted amino (i.e., —NH 2 ) or substituted amino (e.g., —NHR N1 ), where R N1 is independently —OH, —SO 2 OR N2 , —SO 2 R N2 , —SOR N2 , —COOR N2 , optionally substituted alkyl, or optionally substituted aryl, and each R N2 can be optionally substituted alkyl or optionally substituted aryl.
  • substituted amino may be alkylamino, in which the alkyl groups are optionally substituted as described herein for alkyl.
  • an amino group is —NHR N1 , in which R N1 is optionally substituted alkyl.
  • R N1 is optionally substituted alkyl.
  • Non-limiting examples of —NHR N1 , in which R N1 is optionally substituted alkyl include: optionally substituted alkylamino, a proteinogenic amino acid, a non-proteinogenic amino acid, a C 1-6 alkyl ester of a proteinogenic amino acid, and a C 1-6 alkyl ester of a non-proteinogenic amino acid.
  • aminoalkyl represents an alkyl substituted with one, two, or three amino groups, as defined herein. Aminoalkyl may be further optionally substituted as described for alkyl groups.
  • arene-tetrayl represents a tetravalent group that is an aryl group, in which three hydrogen atoms are replaced with valencies. Arene-tetrayl can be optionally substituted as described herein for aryl.
  • aryl represents a mono-, bicyclic, or multicyclic carbocyclic ring system having one or two aromatic rings.
  • Aryl group may include from 6 to 10 carbon atoms. All atoms within an unsubstituted carbocyclic aryl group are carbon atoms.
  • Non-limiting examples of carbocyclic aryl groups include phenyl, naphthyl, 1,2-dihydronaphthyl, 1,2,3,4-tetrahydronaphthyl, fluorenyl, indanyl, indenyl, etc.
  • the aryl group may be unsubstituted or substituted with one, two, three, four, or five substituents independently selected from the group consisting of: alkyl; alkenyl; alkynyl; alkoxy; alkylsulfinyl; alkylsulfenyl; alkylsulfonyl; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; cycloalkenyl; cycloalkynyl; halo; heteroalkyl; heterocyclyl; (heterocyclyl)oxy; hydroxy; nitro; thiol; silyl; and cyano.
  • Each of the substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group.
  • aryl alkyl represents an alkyl group substituted with an aryl group.
  • the aryl and alkyl portions may be optionally substituted as the individual groups as described herein.
  • aryl alkylene represents an aryl alkyl group, in which one hydrogen atom is replaced with a valency.
  • Aryl alkylene may be optionally substituted as described herein for aryl alkyl.
  • arylene represents an aryl group, in which one hydrogen atom is replaced with a valency.
  • Arylene may be optionally substituted as described herein for aryl.
  • aryloxy represents a chemical substituent of formula —OR, where R is an aryl group, unless otherwise specified. In optionally substituted aryloxy, the aryl group is optionally substituted as described herein for aryl.
  • auxiliary moiety represents a monovalent group containing a hydrophilic polymer, a positively charged polymer, or a sugar alcohol.
  • optionally substituted N represents a divalent —N(R N1 )— group or a trivalent —N ⁇ group.
  • the aza group may be unsubstituted, where R N1 is H or absent, or substituted, where R N1 is as defined for “amino,” except R N1 is not H. Two aza groups may be connected to form “diaza.”
  • N-protected amino represents substituted amino, as defined herein, in which at least one substituent is an N-protecting group and the other substituent is H, if N-protected amino is unsubstituted, or a substituent other than H, if N-protected amino is substituted.
  • the term “bulky group,” as used herein, represents any substituent or group of substituents as defined herein, in which the radical bonding to disulfide is a carbon atom that bears one hydrogen atom or fewer if the radical is sp 3 -hybridized carbon or bears no hydrogen atoms if the radical is sp 2 -hybridized carbon.
  • the radical is not sp-hybridized carbon.
  • 5′-5′ cap represents a group of formula R′-Nuc 1 -O-(L p ) n -, where R′ is phosphate, phosphorothioate, phosphorodithioate, phosphotriester, phosphodiester, hydroxyl, or hydrogen; Nuc 1 is a nucleoside; each L P is independently —P( ⁇ X E1 )(—X E2 —R E2A )—O—; and n is 1, 2, or 3;
  • capping group represents a monovalent or a divalent group situated at the 5′- or 3′-terminus of a polynucleotide.
  • the capping group is a terminal phosphoester; diphosphate; triphosphate; an auxiliary moiety; a bioreversible group; a non-bioreversible group; 5′ cap (e.g., 5′-5′ cap); solid support; a linker bonded to a targeting moiety and optionally to one or more (e.g., 1 to 6) auxiliary moieties; or a group —OR′, where R′ is selected from the group consisting of hydrogen, a bioreversible group, non-bioreversible group, solid support, and O-protecting group.
  • Group —OR′, diphosphate, triphosphate, bioreversible group, non-bioreversible group, solid support, and auxiliaty moiety are examples of monovalent capping groups.
  • a terminal phosphoester is an example of a capping group that can be either monovalent, if the terminal phosphoester does not include a linker to a targeting moiety, or divalent, if the terminal phosphoester includes a linker to a targeting moiety.
  • a linker bonded to a targeting moiety (with our without auxiliary moieties) is an example of a divalent capping group.
  • Carbocyclic represents an optionally substituted C 3-16 monocyclic, bicyclic, or tricyclic structure in which the rings, which may be aromatic or non-aromatic, are formed by carbon atoms.
  • Carbocyclic structures include cycloalkyl, cycloalkenyl, cycloalkynyl, and certain aryl groups.
  • carbonyl represents a —C(O)— group.
  • C x-y indicates that the group, the name of which immediately follows the expression, when unsubstituted, contains a total of from x to y carbon atoms. If the group is a composite group (e.g., aryl alkyl), C x-y indicates that the portion, the name of which immediately follows the expression, when unsubstituted, contains a total of from x to y carbon atoms.
  • (C 6-10 -aryl)-C 1-6 -alkyl is a group, in which the aryl portion, when unsubstituted, contains a total of from 6 to 10 carbon atoms, and the alkyl portion, when unsubstituted, contains a total of from 1 to 6 carbon atoms.
  • cyano represents —CN group.
  • cycloaddition reaction represents reaction of two components in which a total of [4n+2] ⁇ electrons are involved in bond formation when there is either no activation, activation by a chemical catalyst, or activation using thermal energy, and n is 1, 2, or 3.
  • a cycloaddition reaction is also a reaction of two components in which [4n] ⁇ electrons are involved, there is photochemical activation, and n is 1, 2, or 3.
  • Representative cycloaddition reactions include the reaction of an alkene with a 1,3-diene (Diels-Alder reaction), the reaction of an alkene with an ⁇ , ⁇ -unsaturated carbonyl (hetero Diels-Alder reaction), and the reaction of an alkyne with an azido compound (e.g., Hüisgen cycloaddition).
  • cycloalkenyl refers to a non-aromatic carbocyclic group having at least one double bond in the ring and from three to ten carbons (e.g., a C 3 -C 10 cycloalkenyl), unless otherwise specified.
  • Non-limiting examples of cycloalkenyl include cycloprop-1-enyl, cycloprop-2-enyl, cyclobut-1-enyl, cyclobut-1-enyl, cyclobut-2-enyl, cyclopent-1-enyl, cyclopent-2-enyl, cyclopent-3-enyl, norbornen-1-yl, norbornen-2-yl, norbornen-5-yl, and norbornen-7-yl.
  • the cycloalkenyl group may be unsubstituted or substituted (e.g., optionally substituted cycloalkenyl) as described for cycloalkyl.
  • cycloalkenyl alkyl represents an alkyl group substituted with a cycloalkenyl group, each as defined herein.
  • the cycloalkenyl and alkyl portions may be substituted as the individual groups defined herein.
  • cycloalkenylene represents a divalent group that is a cycloalkenyl group, in which one hydrogen atom is replaced with a valency. Cycloalkenylene may be optionally substituted as described herein for cycloalkyl. A non-limiting example of cycloalkenylene is cycloalken-1,3-diyl.
  • cycloalkoxy represents a chemical substituent of formula —OR, where R is cycloalkyl group, unless otherwise specified.
  • the cycloalkyl group can be further substituted as defined herein.
  • cycloalkyl refers to a cyclic alkyl group having from three to ten carbons (e.g., a C 3 -C 10 cycloalkyl), unless otherwise specified.
  • Cycloalkyl groups may be monocyclic or bicyclic.
  • Bicyclic cycloalkyl groups may be of bicyclo[p.q.0]alkyl type, in which each of p and q is, independently, 1, 2, 3, 4, 5, 6, or 7, provided that the sum of p and q is 2, 3, 4, 5, 6, 7, or 8.
  • bicyclic cycloalkyl groups may include bridged cycloalkyl structures, e.g., bicyclo[p.q.r]alkyl, in which r is 1, 2, or 3, each of p and q is, independently, 1, 2, 3, 4, 5, or 6, provided that the sum of p, q, and r is 3, 4, 5, 6, 7, or 8.
  • the cycloalkyl group may be a spirocyclic group, e.g., spiro[p.q]alkyl, in which each of p and q is, independently, 2, 3, 4, 5, 6, or 7, provided that the sum of p and q is 4, 5, 6, 7, 8, or 9.
  • Non-limiting examples of cycloalkyl include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, 1-bicyclo[2.2.1,]heptyl, 2-bicyclo[2.2.1,]heptyl, 5-bicyclo[2.2.1,]heptyl, 7-bicyclo[2.2.1,]heptyl, and decalinyl.
  • the cycloalkyl group may be unsubstituted or substituted (e.g., optionally substituted cycloalkyl) with one, two, three, four, or five substituents independently selected from the group consisting of: alkyl; alkenyl; alkynyl; alkoxy; alkylsulfinyl; alkylsulfenyl; alkylsulfonyl; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; cycloalkenyl; cycloalkynyl; halo; heteroalkyl; heterocyclyl; (heterocyclyl)oxy; hydroxy; nitro; thiol; silyl; cyano; ⁇ O; ⁇ S; ⁇ NR′, where R′ is H, alkyl, aryl, or heterocyclyl.
  • Each of the substituents may itself be unsubstituted or substituted with unsubsti
  • cycloalkyl alkyl represents an alkyl group substituted with a cycloalkyl group, each as defined herein.
  • the cycloalkyl and alkyl portions may be optionally substituted as the individual groups described herein.
  • cycloalkylene represents a divalent group that is a cycloalkyl group, in which one hydrogen atom is replaced with a valency.
  • a non-limiting example of cycloalkylene is cycloalkane-1,3-diyl. Cycloalkylene may be optionally substituted as described herein for cycloalkyl.
  • cycloalkynyl refers to a monovalent carbocyclic group having one or two carbon-carbon triple bonds and having from eight to twelve carbons, unless otherwise specified. Cycloalkynyl may include one transannular bond or bridge. Non-limiting examples of cycloalkynyl include cyclooctynyl, cyclononynyl, cyclodecynyl, and cyclodecadiynyl. The cycloalkynyl group may be unsubstituted or substituted (e.g., optionally substituted cycloalkynyl) as defined for cycloalkyl.
  • dihydropyridazine group represents a divalent group obtainable through cycloaddition between 1,2,4,5-tetrazine group and a strained cycloalkenyl.
  • halo represents a halogen selected from bromine, chlorine, iodine, and fluorine.
  • 5-halouridine represents a nucleoside, in which the nucleobase is 5-halouracil of the following structure:
  • R is a bond to the anomeric carbon of the pentafuranose of the nucleoside
  • X is fluoro, chloro, bromo, iodo. In some embodiments, X is bromo or iodo.
  • heteroalkane-tetrayl refers to an alkane-tetrayl group interrupted once by one heteroatom; twice, each time, independently, by one heteroatom; three times, each time, independently, by one heteroatom; or four times, each time, independently, by one heteroatom.
  • Each heteroatom is, independently, O, N, or S. In some embodiments, the heteroatom is O or N.
  • An unsubstituted C X-Y heteroalkane-tetrayl contains from X to Y carbon atoms as well as the heteroatoms as defined herein.
  • the heteroalkane-tetrayl group may be unsubstituted or substituted (e.g., optionally substituted heteroalkane-tetrayl), as described for heteroalkyl.
  • heteroalkane-triyl refers to an alkane-triyl group interrupted once by one heteroatom; twice, each time, independently, by one heteroatom; three times, each time, independently, by one heteroatom; or four times, each time, independently, by one heteroatom.
  • Each heteroatom is, independently, O, N, or S. In some embodiments, the heteroatom is O or N.
  • An unsubstituted CX Y heteroalkane-triyl contains from X to Y carbon atoms as well as the heteroatoms as defined herein.
  • the heteroalkane-triyl group may be unsubstituted or substituted (e.g., optionally substituted heteroalkane-triyl), as described for heteroalkyl.
  • heteroalkyl refers to an alkyl, alkenyl, or alkynyl group interrupted once by one or two heteroatoms; twice, each time, independently, by one or two heteroatoms; three times, each time, independently, by one or two heteroatoms; or four times, each time, independently, by one or two heteroatoms.
  • Each heteroatom is, independently, O, N, or S. In some embodiments, the heteroatom is O or N. None of the heteroalkyl groups includes two contiguous oxygen or sulfur atoms.
  • the heteroalkyl group may be unsubstituted or substituted (e.g., optionally substituted heteroalkyl).
  • the substituent is selected according to the nature and valency of the heteratom.
  • the substituent bonded to the heteroatom, valency permitting is selected from the group consisting of ⁇ O, —N(R N2 ) 2 , —SO 2 OR N3 , —SO 2 R N2 , —SOR N3 , —COOR N3 , an N-protecting group, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, cycloalkynyl, heterocyclyl, orcyano, where each R N2 is independently H, alkyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, or heterocyclyl, and each R N3 is independently alkyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, or heterocyclyl, and each R N3 is independently alky
  • Each of these substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group.
  • the substituent is selected from those described for alkyl, provided that the substituent on the carbon atom bonded to the heteroatom is not Cl, Br, or I. It is understood that carbon atoms are found at the termini of a heteroalkyl group.
  • heteroaryloxy refers to a structure —OR, in which R is heteroaryl. Heteroaryloxy can be optionally substituted as defined for heterocyclyl.
  • heterocyclyl represents a monocyclic, bicyclic, tricyclic, or tetracyclic ring system having fused or bridging 5-, 6-, 7-, or 8-membered rings, unless otherwise specified, containing one, two, three, or four heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur.
  • Heterocyclyl can be aromatic or non-aromatic.
  • Non-aromatic 5-membered heterocyclyl has zero or one double bonds
  • non-aromatic 6- and 7-membered heterocyclyl groups have zero to two double bonds
  • non-aromatic 8-membered heterocyclyl groups have zero to two double bonds and/or zero or one carbon-carbon triple bond.
  • Heterocyclyl groups include from 1 to 16 carbon atoms unless otherwise specified. Certain heterocyclyl groups may include up to 9 carbon atoms.
  • Non-aromatic heterocyclyl groups include pyrrolinyl, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, homopiperidinyl, piperazinyl, pyridazinyl, oxazolidinyl, isoxazolidiniyl, morpholinyl, thiomorpholinyl, thiazolidinyl, isothiazolidinyl, thiazolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, dihydrothienyl, dihydroindolyl, tetrahydroquinolyl, tetrahydroisoquinolyl, pyranyl
  • heterocyclyl i.e., heteroaryl
  • heteroaryl groups include benzimidazolyl, benzofuryl, benzothiazolyl, benzothienyl, benzoxazolyl, furyl, imidazolyl, indolyl, isoindazolyl, isoquinolinyl, isothiazolyl, isothiazolyl, isoxazolyl, oxadiazolyl, oxazolyl, purinyl, pyrrolyl, pyridinyl, pyrazinyl, pyrimidinyl, qunazolinyl, quinolinyl, thiadiazolyl (e.g., 1,3,4-thiadiazole), thiazolyl, thienyl, triazolyl, tetrazolyl, etc.
  • heteroaryl groups include benzimidazolyl, benzofuryl, benzothiazolyl, benzothienyl, benzox
  • heterocyclyl also represents a heterocyclic compound having a bridged multicyclic structure in which one or more carbons and/or heteroatoms bridges two non-adjacent members of a monocyclic ring, e.g., quinuclidine, tropanes, or diaza-bicyclo[2.2.2]octane.
  • heterocyclyl includes bicyclic, tricyclic, and tetracyclic groups in which any of the above heterocyclic rings is fused to one, two, or three carbocyclic rings, e.g., an aryl ring, a cyclohexane ring, a cyclohexene ring, a cyclopentane ring, a cyclopentene ring, or another monocyclic heterocyclic ring.
  • fused heterocyclyls include 1,2,3,5,8,8a-hexahydroindolizine; 2,3-dihydrobenzofuran; 2,3-dihydroindole; and 2,3-dihydrobenzothiophene.
  • the heterocyclyl group may be unsubstituted or substituted with one, two, three, four or five substituents independently selected from the group consisting of: alkyl; alkenyl; alkynyl; alkoxy; alkylsulfinyl; alkylsulfenyl; alkylsulfonyl; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; cycloalkenyl; cycloalkynyl; halo; heteroalkyl; heterocyclyl; (heterocyclyl)oxy; hydroxy; nitro; thiol; silyl; cyano; ⁇ O; ⁇ S; ⁇ NR′, where R′ is H, alkyl, aryl, or heterocyclyl.
  • Each of the substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group.
  • heterocyclyl alkyl represents an alkyl group substituted with a heterocyclyl group, each as defined herein.
  • the heterocyclyl and alkyl portions may be optionally substituted as the individual groups described herein.
  • (heterocyclyl)aza represents a chemical substituent of formula —N(R N1 )(R N2 ), where R N1 is a heterocyclyl group, and R N2 is H, —OH, —NO 2 , —N(R N2 ) 2 , —SO 2 OR N2 , —SO 2 R N2 , —SOR N2 , —COOR N2 , an N-protecting group, alkyl, alkenyl, alkynyl, alkoxy, aryl, arylalkyl, aryloxy, cycloalkyl, cycloalkenyl, heteroalkyl, or heterocyclyl.
  • R N2 is H.
  • heterocyclylene represted a heterocyclyl group, in which one hydrogen atom is replaced with a valency.
  • the heterocyclylene may be optionally substituted in a manner described for heterocyclyl.
  • a non-limiting example of heterocyclylene is heterocycle-1,3-diyl.
  • heterocyclyloxy represents a chemical substituent of formula —OR, where R is a heterocyclyl group, unless otherwise specified.
  • (Heterocyclyl)oxy can be optionally substituted in a manner described for heterocyclyl.
  • hydroxyl and “hydroxy,” as used interchangeably herein, represent an —OH group.
  • immunomodulating polynucleotide represents a polynucleotide construct containing a total of from 6 to 50 contiguous nucleosides covalently bound together by internucleoside bridging groups independently selected from the group consisting of internucleoside phosphoesters and optionally internucleoside abasic spacers.
  • the immunomodulating polynucleotides are capped at 5′- and 3′-termini with 5′- and 3′-capping groups, respectively.
  • the immunomodulating polynucleotides are capable of modulating an innate immune response, as determined by, e.g., a change in the activation of NF ⁇ B or a change in the secretion of at least one inflammatory cytokine or at least one type I interferon in an antigen-presenting cell to which an immunomodulating polynucleotide was delivered (e.g., in comparison to another antigen-presenting cell to which an immunomodulating polynucleotide was not delivered).
  • the immunomodulating polynucleotide may contain a conjugating group or, if the immunomodulating polynucleotide is part of a conjugate, a linker bonded to a targeting moiety and optionally to one or more (e.g., 1 to 6) auxiliary moieties (e.g., polyethylene glycols).
  • the conjugating group or the linker may be part of the phosphotriester or the terminal capping group.
  • immunomodulating polynucleotide represents an immunomodulating polynucleotide capable of activating an innate immune response, as determined by, e.g., an increase in the activation of NF ⁇ B or an increase in the secretion of at least one inflammatory cytokine or at least one type I interferon in an antigen-presenting cell to which an immunostimulating polynucleotide was delivered (e.g., in comparison to another antigen-presenting cell to which an immunostimulating polynucleotide was not delivered).
  • the immunostimulating polynucleotide contains at least one cytidine-p-guanosine (CpG) sequence, in which p is an internucleoside phosphodiester (e.g., phosphate or phosphorothioate) or an internucleoside phosphotriester or phosphothiotriester.
  • CpG-containing immunostimulating polynucleotide can be naturally existing, such as CpG ODNs of bacterial or viral origins, or synthetic.
  • the CpG sequence in the immunostimulating polynucleotide contains 2′-deoxyribose.
  • the CpG sequence in the immunostimulating polynucleotide is unmethylated.
  • the immunostimulating polynucleotide is an oligonucleotide of Formula (A) as provided herein.
  • the immunostimulating polynucleotide is compound of Formula (B) as provided herein.
  • immunosuppressive polynucleotide represents an immunomodulating polynucleotide capable of antagonizing an innate immune response, as determined by e.g., a reduction in the activation of NF ⁇ B or a reduction in the secretion of at least one inflammatory cytokine or at least one type I interferon in an antigen-presenting cell to which an immunosuppressive polynucleotide was delivered (e.g., in comparison to another antigen-presenting cell to which an immunosuppressive polynucleotide was not delivered).
  • internucleoside bridging group represents an internucleoside phosphoester or an internucleoside abasic spacer.
  • nucleoside in which the nucleobase is of the following structure:
  • 5-modified cytidine is 5-halo cytidine (e.g., 5-iodo cytidine or 5-bromo cytidine). In other embodiments, 5-modified cytidine is 5-alkynyl cytidine.
  • nucleoside in which the nucleobase is of the following structure:
  • R is a bond to the anomeric carbon of the pentafuranose of the nucleoside
  • X is halogen, alkyl, alkenyl, alkynyl, cycloalkyl, heterocyclyl, or aryl, provided that the 5-modified uridine is not thymidine.
  • 5-modified uridine is 5-halouridine (e.g., 5-iodouridine or 5-bromouridine).
  • 5-modified uridine is 5-alkynyl uridine.
  • 5-modified uridine is a nucleoside containing 2-deoxyribose.
  • nitro represents an —NO 2 group.
  • non-bioreversible refers to a chemical group that is resistant to degradation under conditions existing inside an endosome. Non-bioreversible groups do not contain thioesters and/or disulfides.
  • nucleobase represents a nitrogen-containing heterocyclic ring bound to the V position of the sugar moiety of a nucleotide or nucleoside. Nucleobases can be unmodified or modified. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
  • Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C or m5c), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-iodo, 5-bromo, 5-tri
  • nucleobases include those disclosed in U.S. Pat. No. 3,687,808; those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John Wiley & Sons, 1990; those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613; and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, pages 289 302, (Crooke et al., ed., CRC Press, 1993).
  • nucleobases are particularly useful for increasing the binding affinity of the hybridized polynucleotides of the invention, including 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine.
  • 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi et al., eds., Antisense Research and Applications 1993, CRC Press, Boca Raton, pages 276-278). These may be combined, in particular embodiments, with 2′-O-methoxyethyl sugar modifications.
  • modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. Pat. Nos. 3,687,808; 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121; 5,596,091; 5,614,617; and 5,681,941.
  • modified nucleobases as used herein, further represents nucleobases, natural or non-natural, which include one or more protecting groups as described herein.
  • nucleoside represents a pentafuranose-nucleobase combination.
  • the pentafuranose is 2-deoxyribose or a modified version thereof, in which position 2 is substituted with OR, R, halo (e.g., F), SH, SR, NH 2 , NHR, NR 2 , or CN, where R is an optionally substituted C 1-6 alkyl (e.g., C 1-6 alkyl or (C 1-6 alkoxy)-C 1-6 -alkyl) or optionally substituted (C 6-14 aryl)-C 1-4 -alkyl.
  • C 1-6 alkyl e.g., C 1-6 alkyl or (C 1-6 alkoxy)-C 1-6 -alkyl
  • C 6-14 aryl optionally substituted-C 1-4 -alkyl.
  • position 2 is substituted with OR or F, where R is C 1-6 alkyl or (C 1-6 -alkoxy)-C 1-6 -alkyl.
  • R is C 1-6 alkyl or (C 1-6 -alkoxy)-C 1-6 -alkyl.
  • the pentafuranose is bonded to a nucleobase at the anomeric carbon.
  • nucleoside refers to a divalent group having the following structure:
  • B 1 is a nucleobase
  • Y is H, halogen (e.g., F), hydroxyl, optionally substituted C 1-6 alkoxy (e.g., methoxy or methoxyethoxy), or a protected hydroxyl group
  • Y 1 is H or C 1-6 alkyl (e.g., methyl); and each of 3′ and 5′ indicate the position of a bond to another group.
  • nucleotide refers to a nucleoside that is bonded to a phosphate, phosphorothioate, or phosphorodithioate.
  • oxo represents a divalent oxygen atom (e.g., the structure of oxo may be shown as ⁇ O).
  • patient represents a human or non-human animal (e.g., a mammal).
  • the subject may be suffering from a tumor (e.g., a liquid tumor or a solid tumor), as determined by a qualified professional (e.g., a doctor or a nurse practitioner) with or without known in the art laboratory test(s) of sample(s) from the patient.
  • a tumor e.g., a liquid tumor or a solid tumor
  • a qualified professional e.g., a doctor or a nurse practitioner
  • Ph represents phenyl
  • phosphoester represents a group containing a phosphate, phosphorothioate, or phosphorodithioate, in which, at least one valency is covalently bonded to a non-hydrogen substituent, provided that at least one non-hydrogen substituent is a group containing at least one nucleoside.
  • a phosphoester, in which two valencies are covalently bonded to nucleoside-containing groups, is an internucleoside phosphoester.
  • a phosphoester may be a group of the following structure:
  • each of X E1 and X E2 is independently O or S;
  • each or R E1 and R E3 is independently hydrogen or a bond to a nucleoside; a sugar analogue of an abasic spacer; a bioreversible group; a non-bioreversible group; an auxiliary moiety; a conjugating group; a linker bonded to a targeting moiety; a linker bonded to a targeting moiety and one or more (e.g., 1 to 6) auxiliary moieties; or the phosphorus atom in a group of formula —P( ⁇ X E1 )(—X E2 —R E2A )—O—,
  • R E2 is hydrogen, a bioreversible group, a non-bioreversible group, an auxiliary moiety, a conjugating group, a linker bonded to a targeting moiety, or a linker bonded to a targeting moiety and one or more (e.g., 1 to 6) auxiliary moieties;
  • R E1 and R E3 are a bond to a group containing at least one nucleoside. If each of R E1 and R E3 is independently a bond to a group containing at least one nucleoside, the phosphoester is an internucleoside phosphoester. If one of R E1 and R E3 is a bond to a group that does not contain a nucleoside, the phosphoester is a terminal phosphoester.
  • phosphodiester refers to a phosphoester, in which, two of the three valencies are substituted with non-hydrogen substituents, while the remaining valency is substituted with hydrogen.
  • the phosphodiester consists of phosphate, phosphorothioate, or phosphorodithioate; one or two bonds to nucleoside(s), abasic spacer(s), and/or phosphoryl group(s); and, if the phosphodiester contains only one bond to a nucleoside, an abasic spacer, or a phosphoryl group, one group independently selected from the group consisting of a bioreversible group; a non-bioreversible group; an auxiliary moiety; a conjugating group; a linker bonded to a targeting moiety; and a linker bonded to a targeting moiety and one or more (e.g., 1 to 6) auxiliary moieties.
  • a terminal phosphodiester includes one bond to a group containing a nucleoside, and one group selected from the group consisting of a bioreversible group; a non-bioreversible group; an auxiliary moiety; a conjugating group; a phosphoryl group; and a linker bonded to a targeting moiety and optionally to one or more (e.g., 1 to 6) auxiliary moieties.
  • An internucleoside phosphodiester includes two bonds to nucleoside-containing groups.
  • a phosphodiester may be a group of the following structure:
  • each of X E1 and X E2 is independently O or S;
  • each or R E1 and R E3 is independently hydrogen or a bond to a nucleoside; a sugar analogue of an abasic spacer; a bioreversible group; a non-bioreversible group; an auxiliary moiety; a conjugating group; a linker bonded to a targeting moiety; a linker bonded to a targeting moiety and one or more (e.g., 1 to 6) auxiliary moieties; or the phosphorus atom in a group of formula —P( ⁇ X E1 )(—X E2 —R E2A )—O—,
  • R E2 is hydrogen, a bioreversible group, a non-bioreversible group, an auxiliary moiety, a conjugating group, a linker bonded to a targeting moiety, or a linker bonded to a targeting moiety and one or more (e.g., 1 to 6) auxiliary moieties;
  • R E1 , R E2 , and R E3 is hydrogen
  • R E1 and R E3 is a bond to a group containing at least one nucleoside.
  • the phosphodiester is an internucleoside phosphodiester. If one and only one of R E1 and R E3 is a bond to a group containing a nucleoside, the phosphodiester is a terminal phosphodiester.
  • phosphoryl refers to a substituent of formula —P( ⁇ X E1 )(—X E2 —R E2A )—O—R E3A ,
  • each of X E1 and X E2 is independently O or S;
  • R E2A is hydrogen, a bioreversible group, a non-bioreversible group, an auxiliary moiety, a conjugating group, a linker bonded to a targeting moiety, or a linker bonded to a targeting moiety and one or more (e.g., 1 to 6) auxiliary moieties; and
  • R E3A is hydrogen or an open valency.
  • phosphotriester refers to a phosphoester, in which all three valences are substituted with non-hydrogen substituents.
  • the phosphotriester consists of phosphate, phosphorothioate, or phosphorodithioate; one or two bonds to nucleoside(s), or abasic spacer(s), and/or phosphoryl group(s); and one or two groups independently selected from the group consisting of a bioreversible group; a non-bioreversible group; an auxiliary moiety; a conjugating group; and a linker bonded to a targeting moiety and optionally to one or more (e.g., 1 to 6) auxiliary moieties.
  • a terminal phosphotriester includes one bond to a group containing a nucleoside and two groups independently selected from the group consisting of a bioreversible group; a non-bioreversible group; an auxiliary moiety; a conjugating group; a phosphoryl group; and a linker bonded to a targeting moiety and optionally to one or more (e.g., 1 to 6) auxiliary moieties.
  • a terminal phosphotriester contains 1 or 0 linkers bonded to a targeting moiety and optionally to one or more (e.g., 1 to 6) auxiliary moieties.
  • An internucleoside phosphotriester includes two bonds to nucleoside-containing groups.
  • a phosphotriester may be a group of the following structure:
  • each of X E1 and X E2 is independently O or S;
  • each or R E1 and R E3 is independently a bond to a nucleoside; a sugar analogue of an abasic spacer; a bioreversible group; a non-bioreversible group; an auxiliary moiety; a conjugating group; a linker bonded to a targeting moiety; a linker bonded to a targeting moiety and one or more (e.g., 1 to 6) auxiliary moieties; or the phosphorus atom in a group of formula —P( ⁇ X E1 )(—X E2 —R E2A )—O—
  • R E2 is a bioreversible group; a non-bioreversible group; an auxiliary moiety; a conjugating group; a linker bonded to a targeting moiety; or a linker bonded to a targeting moiety and one or more (e.g., 1 to 6) auxiliary moieties;
  • R E1 and R E3 are bonds to a group containing at least one nucleoside. If both R E1 and R E3 are bonds to groups containing at least one nucleoside, the phosphotriester is an internucleoside phosphotriester. If one and only one of R E1 and R E3 is a bond to a group containing a nucleoside, the phosphotriester is a terminal phosphotriester.
  • physiological conditions refer to the conditions that may exist inside a living, mammalian, professional antigen-presenting cell.
  • the physiological conditions include temperatures from about 35° C. to about 42° C. and aqueous pH from about 6 to about 8.
  • protecting group represents a group intended to protect a hydroxy, an amino, or a carbonyl from participating in one or more undesirable reactions during chemical synthesis.
  • O-protecting group represents a group intended to protect a hydroxy or carbonyl group from participating in one or more undesirable reactions during chemical synthesis.
  • N-protecting group represents a group intended to protect a nitrogen containing (e.g., an amino or hydrazine) group from participating in one or more undesirable reactions during chemical synthesis.
  • O- and N-protecting groups are disclosed in Greene, “Protective Groups in Organic Synthesis,” 3 rd Edition (John Wiley & Sons, New York, 1999), which is incorporated herein by reference.
  • Exemplary O- and N-protecting groups include alkanoyl, aryloyl, orcarbamyl groups such as formyl, acetyl, propionyl, pivaloyl, t-butylacetyl, 2-chloroacetyl, 2-bromoacetyl, trifluoroacetyl, trichloroacetyl, phthalyl, o-nitrophenoxyacetyl, ⁇ -chlorobutyryl, benzoyl, 4-chlorobenzoyl, 4-bromobenzoyl, t-butyldimethylsilyl, tri-iso-propylsilyloxymethyl, 4,4′-dimethoxytrityl, isobutyryl, phenoxyace
  • O-protecting groups for protecting carbonyl containing groups include, but are not limited to: acetals, acylals, 1,3-dithianes, 1,3-dioxanes, 1,3-dioxolanes, and 1,3-dithiolanes.
  • O-protecting groups include, but are not limited to: substituted alkyl, aryl, and aryl-alkyl ethers (e.g., trityl; methylthiomethyl; methoxymethyl; benzyloxymethyl; siloxymethyl; 2,2,2,-trichloroethoxymethyl; tetrahydropyranyl; tetrahydrofuranyl; ethoxyethyl; 1-[2-(trimethylsilyl)ethoxy]ethyl; 2-trimethylsilylethyl; t-butyl ether; p-chlorophenyl, p-methoxyphenyl, p-nitrophenyl, benzyl, p-methoxybenzyl, and nitrobenzyl); silyl ethers (e.g., trimethylsilyl; triethylsilyl; triisopropylsilyl; dimethylisopropylsilyl; t-butyld
  • N-protecting groups include, but are not limited to, chiral auxiliaries such as protected or unprotected D, L or D, L-amino acids such as alanine, leucine, phenylalanine, and the like; sulfonyl-containing groups such as benzenesulfonyl, p-toluenesulfonyl, and the like; carbamate forming groups such as benzyloxycarbonyl, p-chlorobenzyloxycarbonyl, p-methoxybenzyloxycarbonyl, p-nitrobenzyloxycarbonyl, 2-nitrobenzyloxycarbonyl, p-bromobenzyloxycarbonyl, 3,4-dimethoxybenzyloxycarbonyl, 3,5-dimethoxybenzyl oxycarbonyl, 2,4-dimethoxybenzyloxycarbonyl, 4-methoxybenzyloxycarbonyl, 2-nitro-4,5-dimethoxybenzyloxy
  • N-protecting groups are formyl, acetyl, benzoyl, pivaloyl, t-butylacetyl, alanyl, phenylsulfonyl, benzyl, t-butyloxycarbonyl (Boc), and benzyloxycarbonyl (Cbz).
  • pyrid-2-yl hydrazone represents a group of the structure:
  • each R′ is independently H or optionally substituted C 1-6 alkyl.
  • Pyrid-2-yl hydrazone may be unsubstituted (i.e., each R′ is H).
  • stereochemically enriched refers to a local stereochemical preference for one stereoisomeric configuration of the recited group over the opposite stereoisomeric configuration of the same group.
  • a polynucleotide containing a stereochemically enriched phosphorothioate is a strand, in which a phosphorothioate of predetermined stereochemistry is present in preference to a phosphorothioate of the opposite stereochemistry. This preference can be expressed numerically using a diastereomeric ratio for the phosphorothioate of the predetermined stereochemistry.
  • the diastereomeric ratio for the phosphorothioate of the predetermined stereochemistry is the molar ratio of the diastereomers having the identified phosphorothioate with the predetermined stereochemistry relative to the diastereomers having the identified phosphorothioate with the opposite stereochemistry.
  • the diastereomeric ratio for the phosphorothioate of the predetermined stereochemistry may be greater than or equal to 1.1 (e.g., greater than or equal to 4, greater than or equal to 9, greater than or equal to 19, or greater than or equal to 39).
  • Q-tag refers to a portion of a polypeptide containing glutamine residue that, upon transglutaminase-mediated reaction with a compound containing —NH 2 amine, provides a conjugate containing the portion of polypeptide, in which the glutamine residue includes a side chain modified to include the amide bonded to the compound.
  • Q-tags are known in the art. Non-limiting examples of Q-tags are LLQGG and GGGLLQGG.
  • strained cycloalkenyl refers to a cycloalkenyl group that, if the open valency were substituted with H, has a ring strain energy of at least 16 kcal/mol.
  • sugar analogue represents a divalent or trivalent group that is a C 3-6 monosaccharide or C 3-6 alditol (e.g., glycerol), which is modified to replace two hydroxyl groups with bonds to the oxygen atoms in phosphate, phosphorothioate, or phosphorodithioate, or a capping group.
  • a sugar analogue does not contain a nucleobase capable of engaging in hydrogen bonding with a nucleobase in a complementary strand.
  • a sugar analogue is cyclic or acyclic.
  • Non-limiting examples of sugar analogues are optionally substituted C 2-6 alkylene, optionally substituted C 2-6 alkenylene, optionally substituted C 5 cycloalkane-1,3-diyl, optionally substituted C 5 cycloalkene-1,3-diyl, optionally substituted heterocycle-1,3-diyl (e.g., optionally substituted pyrrolidine-2,5-diyl, optionally substituted tetrahydrofuran-2,5-diyl, or optionally substituted tetrahydrothiophene-2,5-diyl), or optionally substituted (C 1-4 alkyl)-(C 3-8 cycloalkylene) (e.g., optionally substituted (C 1 alkyl)-(C 3 cycloalkylene)).
  • sulfide represents a divalent —S— or ⁇ S group. Disulfide is —S—S—.
  • targeting moiety represents a moiety (e.g., a small molecule, e.g., a carbohydrate) that specifically binds or reactively associates or complexes with a receptor or other receptive moiety associated with a given target cell population (e.g., an antigen-presenting cell (APC; e.g., a professional APC (e.g., B-cell, pDC, or macrophage))).
  • a conjugate of the invention contains a targeting moiety.
  • the targeting moiety can be an antibody or an antigen-binding fragment or an engineered derivative thereof (e.g., Fcab or a fusion protein (e.g., scFv)).
  • the targeting moiety can be a polypeptide.
  • the targeting moiety can be a small molecule (e.g., mannose) or a cluster of small molecules (e.g., a cluster of mannoses).
  • a conjugate of the invention that includes the targeting moiety may exhibit K d of less than 100 nM for the target, to which the targeting moiety bind. K d is measured using methods known in the art, e.g., using surface plasmon resonance (SPR), e.g., using BIACORETM system (GE Healthcare, Little Chalfont, the United Kingdom).
  • 1,2,4,5-tetrazine group represents a group of the following formula
  • R′ is optionally substituted alkyl, optionally substituted aryl, optionally substituted cycloalkyl, optionally substituted heterocyclyl
  • R′′ is optionally substituted alkylene, optionally substituted heteroalkylene, optionally substituted arylene, optionally substituted cycloalkylene, optionally substituted heterocyclylene, or a group —R a —R b —, in which each of R a and R b is independently optionally substituted alkylene, optionally substituted heteroalkylene, optionally substituted arylene, optionally substituted cycloalkylene, or optionally substituted heterocyclylene.
  • therapeutic effect refers to a local or systemic effect in a subject, particularly mammals, and more particularly humans, caused by a pharmacologically active substance.
  • the term thus means any substance intended for use in the diagnosis, cure, mitigation, treatment or prevention of disease or in the enhancement of desirable physical or mental development and conditions in an animal or human.
  • therapeuticically effective amount” or “therapeutically effective dose,” as used herein, represents the quantity of an immunomodulating polynucleotide or a conjugate necessary to ameliorate, treat, or at least partially arrest the symptoms of a disease to be treated. Amounts effective for this use depend on the severity of the disease and the weight and general state of the subject. Typically, dosages used in vitro may provide useful guidance in the amounts useful for in vivo administration of the pharmaceutical composition, and animal models may be used to determine effective dosages for treatment of a particular disease.
  • thiocarbonyl represents a C( ⁇ S) group.
  • thioheterocyclylene represents a group —S—R—, where R is heterocyclylene.
  • Thioheterocyclylene may be optionally substituted in a manner described for heterocyclyl.
  • thiol represents an —SH group.
  • treating is intended to refer to obtaining beneficial or desired results, e.g., clinical results, in a patient by administering the polynucleotide or conjugate of the invention to the patient.
  • beneficial or desired results may include alleviation or amelioration of one or more symptoms of a disease or condition; diminishment of extent of a disease or condition; stabilization (i.e., not worsening) of a disease or condition; prevention of the spread of a disease or condition; delay or slowing the progress of a disease or condition; palliation of a disease or condition; and remission (whether partial or total).
  • “Palliating” a disease or condition means that the extent and/or undesirable clinical manifestations of the disease or condition are lessened and/or time course of the progression is slowed, as compared to the extent or time course in the absence of the treatment with the polynucleotide or conjugate of the invention.
  • triazolocycloalkenylene refers to the heterocyclylenes containing a 1,2,3-triazole ring fused to an 8-membered ring, all of the endocyclic atoms of which are carbon atoms, and bridgehead atoms are sp 2 -hybridized carbon atoms. Triazocycloalkenylenes can be optionally substituted in a manner described for heterocyclyl.
  • triazoloheterocyclylene refers to the heterocyclylenes containing a 1,2,3-triazole ring fused to an 8-membered ring containing at least one heteroatom.
  • the bridgehead atoms in triazoloheterocyclylene are carbon atoms.
  • Triazoloheterocyclylenes can be optionally substituted in a manner described for heterocyclyl.
  • immunomodulating polynucleotide encompass salts of the immunomodulating polynucleotide, immunostimulating polynucleotide, immunosuppressive polynucleotide and conjugate, respectively.
  • the terms “immunomodulating polynucleotide,” “immunostimulating polynucleotide,” “immunosuppressive polynucleotide,” and “conjugate” encompasses both the protonated, neutral form (P—XH moiety, where X is O or S) of a phosphate, phosphorothioate, or phosphorodithioate and the deprotonated, ionic form (P—X ⁇ moiety, where X is O or S) of a phosphate, phosphorothioate, or phosphorodithioate.
  • the phosphoesters and phosphodiesters described as having one or more of R E1 , R E2 , and R E3 as hydrogen encompass salts, in which the phosphate, phosphorothioate, or phosphorodithioate is present in a deprotonated, ionic form.
  • innate immune response and “innate immunity” are recognized in the art, and refer to non-specific defense mechanism a body's immune system initiates upon recognition of pathogen-associated molecular patterns, which involves different forms of cellular activities, including cytokine production and cell death through various pathways.
  • innate immune responses include cellular responses to a CpG-containing immunostimulating polynucleotide mediated by toll-like receptor 9 (TLR9), which include, without limitation, increased production of inflammation cytokines (e.g., type I interferon or IL-10 production), activation of the NF ⁇ B pathway, increased proliferation, maturation, differentiation and/or survival of immune cells, and in some cases, induction of cell apoptosis.
  • TLR9 toll-like receptor 9
  • Activation of the innate immunity can be detected using methods known in the art, such as measuring the (NF)- ⁇ B activation.
  • adaptive immune response and “adaptive immunity” are recognized in the art, and refer to antigen-specific defense mechanism a body's immune system initiates upon recognition of a specific antigen, which include both humoral response and cell-mediated responses.
  • adaptive immune responses include cellular responses that is triggered and/or augmented by a CpG-containing immunostimulating polynucleotide.
  • the immunostimulating polynucleotide or a portion thereof is the antigen target of the antigen-specific adaptive immune response.
  • the immunostimulating polynucleotide is not the antigen target of the antigen-specific adaptive immune response, but nevertheless augments the adaptive immune response.
  • Activation of an adaptive immune response can be detected using methods known in the art, such as measuring the antigen-specific antibody production, or the level of antigen-specific cell-mediated cytotoxicity.
  • Toll-like receptor (or “TLR”) is recognized in the art, and refers to a family of pattern recognition receptors that were initially identified as sensors of the innate immune system that recognize microbial pathogens. TLRs recognize distinct structures in microbes, often referred to as “PAMPs” (pathogen associated molecular patterns). Ligand binding to TLRs invokes a cascade of intra-cellular signaling pathways that induce an innate immune response and/or adaptive immune response. As used herein, the term “toll-like receptor” or “TLR” also refers to a functional fragment of a toll-like receptor protein expressed by a cell.
  • TLR-1 TLR-1, -2, -3, -4, -5, -6, -7/8, and -9.
  • Human genes encoding TLRs are known.
  • TLR9 Toll-like receptor 9
  • CD289 cluster of differentiation 289
  • TLR9 is an important receptor expressed in immune system cells including dendritic cells (DCs), B lymphocytes, macrophages, natural killer cells, and other antigen presenting cells. TLR9 activation triggers signaling cascades that bridges the innate and adaptive immunity. Martinez-Campos et al. Viral Immunol., 30:98-105 (2016); Notley et al., Sci.
  • Natural TLR-9 agonists include unmethylated cytosine-guanine dinucleotide (CpG)-containing oligodeoxynucleotides (CpG ODNs).
  • TLR-9 ligand finding use in the present disclosure include, but are not limited to, naturally existing or synthetic CpG ODNs, and other CpG-containing immunostimulating polynucleotide and/or immunoconjugates as provided herein.
  • Activation of the TLR9 signaling pathway can be detected using methods known in the art, such as measuring recruitment of myeloid differentiation antigen 88 (MyD88), activation of nuclear factor (NF)- ⁇ B, c-Jun N-terminal kinase (JNK), and p38 mitogen-activated protein kinase (MAPK) signaling pathways, activation of interferon regulatory factor-7, expression level of one or more of cytokines such as type I interferons (IFNs), interleukin (IL)-6, IL-10, and IL-12, activation of one or more immune cell populations such as NK cells, natural killer T cells, monocytes, and level of cytotoxic lymphocyte (CTL) and T helper-1 (Th1) responses, and the level of immunoglobulin secretion.
  • IFNs type I interferons
  • IL-6 interleukin-6
  • IL-10 interleukin-6
  • IL-12 IL-12
  • immune cell populations such as NK cells, natural killer
  • TLR-expressing cell refers to a cell that expresses a toll-like receptor and is capable of activating the toll-like receptor signaling pathway upon binding of the toll-like receptor to an agonist.
  • the toll-like receptor may be expressed on the cell surface, and/or on the membrane of one or more intracellular compartments of the cell, such as the endosome or phagosome.
  • a TLR-expressing cell may further express one or more cell surface antigens other than the toll-like receptor.
  • Certain immune cells express TLRs, and activation of the TLR signaling pathway in the immune cells elicits an innate immune response, and/or an adaptive immune response. Immune cells activated by the TLR signaling pathway can help eliminate other diseased cells from the body.
  • TLR9-expressing cells include but are not limited to dendritic cells (DCs), B cells, T cells, Langerhans cells, keratinocytes, mast cells, endothelial cells, myofibroblast cells, and primary fibroblast. Determining whether a cell expresses any toll-like receptor (e.g., TLR9) can be performed using methods known in the art, such as detecting mRNA of the toll-like receptor in a cell.
  • immune cell refers to any cell involved in a host defense mechanism, such as cells that produces pro-inflammatory cytokines, and cells that participate in tissue damage and/or disease pathogenesis.
  • immune cells include, but are not limited to, T cells, B cells, natural killer cells, neutrophils, mast cells, macrophages, antigen-presenting cells (APC), basophils, and eosinophils.
  • antigen presenting cell refers to a heterogeneous group of immune cells that mediate the cellular immune response by processing and presenting antigens for recognition by certain lymphocytes such as T cells.
  • antigen presenting cells include, but are not limited to, professional antigen presenting cells including, for example, B cells, monocytes, dendritic cells, and Langerhans cells, as well as other antigen presenting cells including, for example, keratinocytes, endothelial cells, astrocytes, fibroblasts, and oligodendrocytes.
  • antigen presenting cell includes antigen presenting cells found in vivo and those found in in vitro cell cultures derived from the in vivo cells.
  • antigen presenting cells also include a APC that is artificially modified, such as genetically modified to express a toll-like receptor (e.g., TLR9) or to modulate expression level of a toll-like receptor (e.g., TLR9).
  • DC dendritic cells
  • APCs antigen-sensing and antigen-presenting cells
  • Human DC are divided into three major subsets: plasmacytoid DC (pDC), myeloid DC (mDC) and monocyte-derived DC (MDDC).
  • pDC plasmacytoid DC
  • mDC myeloid DC
  • MDDC monocyte-derived DC
  • Subsets of DCs can be identified on the basis of distinct TLR expression patterns.
  • the myeloid or “conventional” subset of DC expresses TLRs 1-8 when stimulated, and a cascade of activation markers (e.g. CD80, CD86, MHC class I and II, CCR7), pro-inflammatory cytokines, and chemokines are produced.
  • a cascade of activation markers e.g. CD80, CD86, MHC class I and II, CCR7
  • pro-inflammatory cytokines e.g. CD80, CD86, MHC class I and II, CCR7
  • chemokines e.g. CD80, CD86, MHC class I and II, CCR7
  • antigen refers to a molecule or an antigenic fragment thereof capable of eliciting an immune response, including both an innate immune response and an adaptive immune response.
  • antigens can be proteins, peptides, polysaccharides, lipids, nucleic acids, especially RNA and DNA, nucleotides, and other biological or biochemical substances.
  • elicit an immune response refers to the stimulation of immune cells in vivo in response to a stimulus, such as an antigen.
  • the immune response consists of both cellular immune response, e.g., T cell and macrophage stimulation, and humoral immune response, e.g., B cell and complement stimulation and antibody production. Immune response may be measured using techniques well-known in the art, including, but not limited to, antibody immunoassays, proliferation assays, and others.
  • an antigenic fragment as used herein is able to complex with an antigen binding molecule, e.g., an antibody, in a specific reaction.
  • the specific reaction referred to herein indicates that the antigen or antigenic fragment will react, in a highly selective manner, with its corresponding antibody and not with the multitude of other antibodies which may be evoked by other antigens.
  • the specificity of such reaction is determined by the presence of one or more epitopes (immunogenic determinants) in the antigen.
  • an antigen or antigenic fragment thereof may have one epitope, or have more than one epitopes.
  • T cell epitope refers to any epitopes of antigens produced by a T cell.
  • tumor associated antigen refers to an antigen expressed by a cancer cell or in the stroma of a solid tumor in a cancer patient receiving the treatment or preventive care as provided herein (e.g., receiving a therapeutic dose of an immunostimulating polynucleotide or a CpG-Ab immunoconjugate).
  • the TAA may or may not be targeted in the treatment or the preventive care provided herein.
  • the TAA does not have to be overexpressed, mutated or misregulated on cancer cell but can have same features as the TAA would have in a normal cell. In some embodiments, the TAA can be overexpressed, mutated or misregulated in cancer cell.
  • the TAA can be a protein, nucleic acid, lipid or other antigen.
  • the TAA can be a cell-surface expressed TAA, an intracellular TAA or an intranuclear TAA.
  • the TAA can be expressed in the stroma of a solid tumor mass.
  • stroma refers to components in a solid tumor mass other than a cancer cell.
  • the stroma can include fibroblasts, epithelial cells, other blood vessel components or extracellular matrix components.
  • stroma does not include components of the immune system, such as immune cells (e.g., B-cells, T-cells, dendritic cells, macrophages, natural killer cells, and the like)).
  • immune cells e.g., B-cells, T-cells, dendritic cells, macrophages, natural killer cells, and the like.
  • TAAs are known in the art. Identifying TAA can be performed using methods known in the art, such as disclosed in Zhang et al. Methods Mol. Biol., 520:1-10 (2009); the content of which is enclosed herein by reference.
  • antibody refers to a polypeptide of the immunoglobulin family that is capable of binding a corresponding antigen non-covalently, reversibly, and in a specific manner.
  • a naturally occurring IgG antibody is a tetramer comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds.
  • Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region.
  • the heavy chain constant region is comprised of three domains, CH1, CH2 and CH3.
  • Each light chain is comprised of a light chain variable region (abbreviated herein as VL) and a light chain constant region.
  • the light chain constant region is comprised of one domain, CL.
  • CL The VH and VL regions can be further subdivided into regions of hyper variability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR).
  • CDR complementarity determining regions
  • FR framework regions
  • Each VH and VL is composed of three CDRs and four FRs arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4.
  • the variable regions of the heavy and light chains contain a binding domain that interacts with an antigen.
  • the constant regions of the antibodies may mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system.
  • antibodies include, but are not limited to, monoclonal antibodies, human antibodies, humanized antibodies, camelid antibodies, chimeric antibodies, and anti-idiotypic (anti-Id) antibodies (including, e.g., anti-Id antibodies to antibodies of the invention).
  • the antibodies can be of any isotype/class (e.g., IgG, IgE, IgM, IgD, IgA and IgY), or subclass (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2).
  • variable domains of both the light (VL) and heavy (VH) chain portions determine antigen recognition and specificity.
  • the constant domains of the light chain (CL) and the heavy chain (CH1, CH2 or CH3) confer important biological properties such as secretion, transplacental mobility, Fc receptor binding, complement binding, and the like.
  • the numbering of the constant region domains increases as they become more distal from the antigen binding site or amino-terminus of the antibody.
  • the N-terminus is a variable region and at the C-terminus is a constant region; the CH3 and CL domains actually comprise the carboxy-terminal domains of the heavy and light chain, respectively.
  • antibody may also refer to an antigen binding fragment of an antibody molecule.
  • antigen binding fragment refers to one or more portions of an antibody that retain the ability to specifically interact with (e.g., by binding, steric hindrance, stabilizing/destabilizing, spatial distribution) an epitope of an antigen.
  • binding fragments include, but are not limited to, single-chain Fvs (scFv), disulfide-linked Fvs (sdFv), Fab fragments, F(ab′) fragments, a monovalent fragment consisting of the VL, VH, CL and CH1 domains; a F(ab)2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; a Fd fragment consisting of the VH and CH1 domains; a Fv fragment consisting of the VL and VH domains of a single arm of an antibody; a dAb fragment (Ward et al. Nature, 341:544-546 (1989)), which consists of a VH or VL domain; a single domain antibody (VHH), and an isolated complementarity determining region (CDR), or other epitope-binding fragments of an antibody.
  • scFv single-chain Fvs
  • sdFv disulfide-linked F
  • the term “specifically binds,” “selectively binds” or the like refers to a chemical interaction between two molecules, compounds, cells and/or particles wherein the first entity binds to the second, target entity with greater specificity and affinity than it binds to a third entity which is a non-target.
  • “specific binding” can refer to an affinity of the first entity for the second target entity which is at least 10 times, at least 50 times, at least 100 times, at least 500 times, at least 1000 times or greater than the affinity for the third non-target entity.
  • “specific binding” is used in the context of describing the interaction between an antigen (or an antigenic fragment thereof) and an antibody (or antigen-binding fragment thereof).
  • “specific binding” refers to binding of the antibody to a predetermined antigen with a disassociation constant (KD) of 10 ⁇ 5 M or less, 10 ⁇ 6 M or less, or 10 ⁇ 7 M or less, or binding of an antibody to a predetermined antigen with a KD that is at least twofold less than its KD for binding to a nonspecific antigen other than the predetermined antigen.
  • KD disassociation constant
  • specific binding can be used to determine the presence of the predetermined antigen in a heterogeneous population of proteins and other biologies, e.g., in a biological sample, e.g., a blood, serum, plasma or tissue sample.
  • the antibodies or binding agents with a particular binding specificity bind to a particular antigen at least two times the background and do not substantially bind in a significant amount to other antigens present in the sample.
  • the antibody or binding agents with a particular binding specificity bind to a particular antigen at least two, three, four, five, six, seven, eight, nine or ten times the background and do not substantially bind in a significant amount to other antigens present in the sample.
  • Specific binding to an antibody or binding agent under such conditions may require the antibody or agent to have been selected for its specificity for a particular protein.
  • this selection may be achieved by subtracting out antibodies that cross-react with molecules from other species (e.g., mouse or rat) or other subtypes.
  • antibodies or antibody fragments are selected that cross-react with certain desired molecules.
  • cancer refers to the presence of cells possessing characteristics typical of cancer-causing cells, such as uncontrolled proliferation, immortality, metastatic potential, rapid growth and proliferation rate, and certain characteristic morphological features. In some embodiments, such cells exhibit such characteristics in part or in full due to the expression and activity of immune checkpoint inhibitors, such as PD-1, PD-L1, and/or CTLA-4.
  • Cancer cells are often in the form of a solid tumor, which is detectable on the basis of tumor mass, e.g., by procedures such as CAT scan, MR imaging, X-ray, ultrasound or palpation, and/or which is detectable because of the expression of one or more cancer-specific antigens in a sample obtainable from a patient.
  • a solid tumor does not need to have measurable dimensions.
  • Cancer cells may also in the form of a liquid tumor, which cancer cells may exist alone or disseminated within an animal.
  • the terms “disseminated tumor” and “liquid tumor” are used interchangeably, and include, without limitation, leukemia and lymphoma and other blood cell cancers.
  • leukemia refers to a type of cancer of the blood or bone marrow characterized by an abnormal increase of immature white blood cells called “blasts.” Leukemia is a broad term covering a spectrum of diseases. In turn, it is part of the even broader group of diseases affecting the blood, bone marrow, and lymphoid system, which are all known as hematological neoplasms. Leukemias can be divided into four major classifications, acute lymphocytic (or lymphoblastic) leukemia (ALL), acute myelogenous (or myeloid or non-lymphatic) leukemia (AML), chronic lymphocytic leukemia (CLL), and chronic myelogenous leukemia (CML). Further types of leukemia include Hairy cell leukemia (HCL), T-cell prolymphocytic leukemia (T-PLL), large granular lymphocytic leukemia, and adult T-cell leukemia.
  • HCL Hairy cell leukemia
  • lymphomas refers to a group of blood cell tumors that develop from lymphatic cells.
  • the two main categories of lymphomas are Hodgkin lymphomas (HL) and non-Hodgkin lymphomas (NHL) Lymphomas include any neoplasms of the lymphatic tissues.
  • the main classes are cancers of the lymphocytes, a type of white blood cell that belongs to both the lymph and the blood and pervades both.
  • cancer includes premalignant as well as malignant cancers, and also includes primary tumors (e.g., those whose cells have not migrated to sites in the subject's body other than the site of the original tumor) and secondary tumors (e.g., those arising from metastasis, the migration of tumor cells to secondary sites that are different from the site of the original tumor), recurrent cancer and refractory cancer.
  • primary tumors e.g., those whose cells have not migrated to sites in the subject's body other than the site of the original tumor
  • secondary tumors e.g., those arising from metastasis, the migration of tumor cells to secondary sites that are different from the site of the original tumor
  • the terms “cancer recurrence” and “cancer relapse” are used interchangeably and refer to the return of a sign, symptom or disease after a remission.
  • the recurrent cancer cells may re-appear in the same site of the primary tumor or in another location, such as in secondary cancer.
  • the cancer cells may re-appear in the same diseased form as the primary cancer or a different diseased form.
  • a primary cancer is a solid tumor
  • the recurrent cancer is a liquid tumor.
  • a primary cancer is a liquid tumor
  • the recurrent cancer is a solid tumor.
  • the primary cancer and the recurrent cancer are both solid tumors, or both liquid tumors.
  • the recurrent tumor expresses at least one tumor associated antigen that is also expressed by the primary tumor.
  • refractory cancer refers to a cancer that does not respond to a treatment, for example, a cancer that is resistant at the beginning of treatment (e.g., treatment with an immunotherapy) or a cancer that may become resistant during treatment.
  • respond refers to an anti-cancer response, e.g. in the sense of reduction of tumor size or inhibiting tumor growth.
  • the terms can also refer to an improved prognosis, for example, as reflected by an increased time to recurrence, which is the period to first recurrence censoring for second primary cancer as a first event or death without evidence of recurrence, or an increased overall survival, which is the period from treatment to death from any cause.
  • evaluating the likelihood that a tumor or subject will exhibit a favorable response is equivalent to evaluating the likelihood that the tumor or subject will not exhibit favorable response (i.e., will exhibit a lack of response or be non-responsive).
  • cancers include, but are not limited to, B cell cancer, e.g., multiple myeloma, Waldenstrom's macroglobulinemia, the heavy chain diseases, such as, for example, alpha chain disease, gamma chain disease, and mu chain disease, benign monoclonal qammopathy, and immunocytic amyloidosis, melanomas, breast cancer, lung cancer, bronchus cancer, colorectal cancer, prostate cancer, pancreatic cancer, stomach cancer, ovarian cancer, urinary bladder cancer, brain or central nervous system cancer, peripheral nervous system cancer, esophageal cancer, cervical cancer, uterine or endometrial cancer, cancer of the oral cavity or pharynx, liver cancer, kidney cancer, testicular cancer, biliary tract cancer, small bowel or appendix cancer, salivary gland cancer, thyroid gland cancer, adrenal gland cancer, osteosarcoma, chondrosarcoma, cancer of hematologic tissues, and the like.
  • B cell cancer e.g
  • cancers are epithlelial in nature and include but are not limited to, bladder cancer, breast cancer, cervical cancer, colon cancer, gynecologic cancers, renal cancer, laryngeal cancer, lung cancer, oral cancer, head and neck cancer, ovarian cancer, pancreatic cancer, prostate cancer, or skin cancer.
  • the cancer is breast cancer, prostate cancer, lung cancer, or colon cancer.
  • the epithelial cancer is non-small-cell lung cancer, nonpapillary renal cell carcinoma, cervical carcinoma, ovarian carcinoma (e.g., serous ovarian carcinoma), or breast carcinoma.
  • the epithelial cancers may be characterized in various other ways including, but not limited to, serous, endometrioid, mucinous, clear cell, Brenner, or undifferentiated.
  • cancer therapy refers to those therapies or agents that can exert anti-tumor effect or have an anti-tumor activity.
  • anti-tumor effect or anti-tumor activity can be exhibited as a reduction in the rate of tumor cell proliferation, viability, or metastatic activity.
  • a possible way of showing anti-tumor activity is to show a decline in growth rate of abnormal cells that arises during therapy or tumor size stability or reduction.
  • Such activity can be assessed using accepted in vitro or in vivo tumor models, including but not limited to xenograft models, allograft models, MMTV models, and other known models known in the art to investigate anti-tumor activity.
  • the term “prevent”, “preventing” or “prevention” of any disease or disorder means the prevention of the onset, recurrence or spread, in whole or in part, of the disease or condition as described herein, or a symptom thereof.
  • a subject is “in need of” a treatment if such subject would benefit biologically, medically or in quality of life from such treatment.
  • therapeutic agent is art-re cognized and refers to any substance that, upon administration to a subject in need thereof, is biologically, physiologically, or pharmacologically active, and acts locally or systemically to exert a beneficial therapeutic effect to the subject.
  • immunoconjugate or “antibody-drug-conjugate (ADC)” as used herein refers to the linkage of an antigen binding moiety (e.g., an antibody or an antigen binding fragment thereof) with an immunomodulatory polynucleotide as described herein.
  • the linkage can be covalent bonds, or non-covalent interactions, and can include chelation.
  • linkers known in the art or provided herein, can be employed in order to form the immunoconjugate.
  • the immunoconjugate is a conjugate of Formula (C) as provided herein.
  • antigen binding moiety refers to a moiety capable of binding specifically to an antigen, and includes but is not limited to antibodies and antigen binding fragments.
  • CpG-Ab immunoconjugate or “CpG-Ab” as used herein refers to the linkage of an antibody (Ab) or an antigen binding fragment thereof with a CpG-containing immunostimulating polynucleotide as described herein.
  • T-cell agonist refers to any agent that selectively stimulates the proliferation, differentiation, and/or survival of T cells from a mixed starting population of cells. Thus, the resulting cell population is enriched with an increased number of T cells compared with the starting population of cells.
  • T cell agonists finding use in the present disclosure include but are not limited to antigen molecules specifically binding to T cell receptors (TCRs), as well as T cell co-stimulatory molecules.
  • T cell co-stimulatory molecules includes but are not limited to OX40, CD2, CD27, CDS, ICAM-1, LFA-1 (CD11a/CD18), ICOS (CD278), 4-1BB (CD137), GITR, CD30, CD40, BAFFR, HVEM, CD7, LIGHT, NKG2C, SLAMF7, NKp80, CD160, B7-H3 and CD83 ligand.
  • the T-cell agonist is an antibody against a T cell co-stimulatory molecule.
  • the T cell agonist is a tumor associated antigen (TAA).
  • T cell agonist is a pathogenic antigen.
  • an “immune checkpoint” or “immune checkpoint molecule” is a molecule in the immune system that modulates a signal.
  • An immune checkpoint molecule can be a stimulatory checkpoint molecule, i.e., turn up a signal, or inhibitory checkpoint molecule, i.e., turn down a signal.
  • immune checkpoint is a protein expressed either by T cells or by antigen presenting cells (APC). Certain types of cancer cells express immune checkpoint proteins to evade immune clearance. Use of immune checkpoint modulators to inhibit the interaction between the immune checkpoint protein expressed by cancer cells and the immune checkpoint protein expressed by T cells has proved effective in certain cancer treatment.
  • an “immune checkpoint modulator” is an agent capable of altering the activity of an immune checkpoint in a subject.
  • an immune checkpoint modulator alters the function of one or more immune checkpoint molecules including, but not limited to, PD-1, PD-L1, PD-L2, TIM-3, LAG-3, CEACAM-1, CEACAM-5, VISTA, BTLA, TIGIT, LAIR1, CD160, CD47, 2B4 and TGFR.
  • the immune checkpoint modulator may be an agonist or an antagonist of the immune checkpoint.
  • the immune checkpoint modulator is an immune checkpoint binding protein (e.g., an antibody, antibody Fab fragment, divalent antibody, antibody drug conjugate, scFv, fusion protein, bivalent antibody, or tetravalent antibody).
  • the immune checkpoint modulator is a small molecule.
  • the immune checkpoint modulator is an anti-PDI or an anti-PD-LI antibody.
  • target refers to the process that promotes the arrival of a delivered agent (such as an immunostimulating polynucleotide) at a specific organ, tissue, cell and/or intracellular compartment (referred to as the targeted location) more than any other organ, tissue, cell or intracellular compartment (referred to as the non-target location).
  • a delivered agent such as an immunostimulating polynucleotide
  • Targeted delivery can be detected using methods known in the art, for example, by comparing the concentration of the delivered agent in a targeted cell population with the concentration of the delivered agent at a non-target cell population after systemic administration. As provided herein, targeted delivery results in at least 2 fold higher concentration at a targeted location as compared to a non-target location.
  • Targeted delivery may be achieved by specific binding of the targeting moiety to an receiving moiety associated with a targeted cell.
  • an receiving moiety associated with a targeted cell may be located on the surface or within the cytosol of the targeted cell.
  • the receiving moiety is an antigen associated with the targeted cell.
  • abnormal when used in the context of organisms, tissues, cells or components thereof, refers to those organisms, tissues, cells or components thereof that differ in at least one observable or detectable characteristic (e.g., age, treatment, time of day, etc.) from those organisms, tissues, cells or components thereof that display the “normal” (expected) respective characteristic. Characteristics which are normal or expected for one cell or tissue type, might be abnormal for a different cell or tissue type. In some embodiments, an abnormal cell is a cancer cell.
  • combination therapy refers to the administration of two or more therapeutic agents to treat a condition or disorder (e.g., cancer) described in the present disclosure.
  • Such administration encompasses co-administration of these therapeutic agents in a substantially simultaneous manner, such as administering a single formulation having a fixed ratio of therapeutic agents or in separate formulations (e.g., capsules and/or intravenous formulations) for each therapeutic agent.
  • such administration also encompasses use of each type of therapeutic agent in a sequential or separate manner, either at approximately the same time or at different times.
  • Such administration also encompasses each component being formulated as a separate formulation that can be administered at different times and/or through different administration routes.
  • the treatment regimen of the combination therapy will provide beneficial therapeutic effects in treating the conditions or disorders described herein.
  • co-administering refers to the act of administering two or more therapeutic agents (e.g., an immunoconjugate and an immune checkpoint modulator), compounds, therapies, or the like, at or about the same time.
  • Co-administering may refer to simultaneous administration, where the different therapeutic agents of the present disclosure, e.g., an immunoconjugate, T cell agonists, immune checkpoint modulators, or other chemotherapeutics, may be combined into the same formulation, or formulated separately for simultaneous administration to a subject.
  • Co-administering may also refer to sequential administration.
  • Co-administering may also refer to the situation where two or more agents are administered to different regions of the body or via different delivery schemes, e.g., where a first agent is administered systemically and a second agent is administered intratumorally, or where a first agent is administered intratumorally and a second agent is administering systemically into the blood or proximally to the tumor.
  • Co-administering may also refer to two or more agents administered via the same delivery scheme, e.g., where a first agent is administered intratumorally and a second agent is administered intratumorally.
  • Tumoral injection refers to administration of an agent as provided herein directly into the tumor cellular mass and/or the tumor microenvironment.
  • tumor microenvironment includes the neoplasia milieu that creates a structural and/or functional environment for the neoplastic process to survive, expand, or spread.
  • a tumor microenvironment is constituted by the cells, molecules, fibroblasts, extracellular matrix and blood vessels that surround and feed one or more neoplastic cells forming the tumor.
  • tumor vasculature examples include, but are not limited to, tumor vasculature, tumor infiltrating lymphocytes, fibroblast reticular cells, endothelial progenitor cells (EPC), cancer-associated fibroblasts, pericytes, other stromal cells, components of the extracellular matrix (ECM), dendritic cells, antigen presenting cells, T-cells, regulatory T-cells, macrophages, neutrophils, and other immune cells located proximal to a tumor.
  • EPC endothelial progenitor cells
  • ECM extracellular matrix
  • dendritic cells antigen presenting cells
  • T-cells regulatory T-cells
  • macrophages macrophages
  • neutrophils neutrophils
  • Examples of cellular functions affecting the tumor microenvironment include, but are not limited to, production of cytokines and/or chemokines, response to cytokines, antigen processing and presentation of peptide antigen, regulation of leukocyte chemotaxis and migration, regulation of gene expression, complement activation, regulation of signaling pathways, cell-mediated cytotoxicity, cell-mediated immunity, humoral immune responses, and other innate or adaptive immune responses. Measuring the effect of modulating of these cellular functions
  • the terms “subject,” “patient,” “individual” and the like are used interchangeably herein, and refer to any animal or cells thereof whether in vitro or in vivo, amendable to the methods provided herein.
  • the patient, subject or individual is a mammal, such as a human, or other animals, such as wild animals (such as herons, storks, cranes, etc.), livestock (such as ducks, geese, etc.) or experimental animals (such as orangutans, monkeys, rats, mice, rabbits, guinea pigs, marmots, ground squirrels, etc.).
  • survival as used in the context of cancer includes any of the following: survival until mortality, also known as overall survival (wherein said mortality may be either irrespective of cause or tumor related); “recurrence-free survival” (wherein the term recurrence shall include both localized and distant recurrence); metastasis free survival; disease free survival (wherein the term disease shall include cancer and diseases associated therewith).
  • the length of said survival may be calculated by reference to a defined start point (e.g. time of diagnosis or start of treatment) and end point (e.g. death, recurrence or metastasis).
  • criteria for efficacy of treatment can be expanded to include response to chemotherapy, probability of survival, probability of metastasis within a given time period, and probability of tumor recurrence.
  • the invention provides immunomodulating (e.g., immunostimulating) polynucleotides and conjugates containing a targeting moiety and one or more immunomodulating (e.g., immunostimulating) polynucleotides.
  • the immunomodulating polynucleotides may contain a 5-modified uridine or 5-modified cytidine.
  • the inclusion of 5-modified uridine (e.g., 5-ethynyl-uridine) at the 5′-terminus of the immunomodulating polynucleotides may enhance the immunomodulating properties of the polynucleotides.
  • the immunomodulating polynucleotides may be shorter (e.g., contain a total of from 6 to 16 nucleotides or from 12 to 14 nucleotides) than typical CpG ODNs, which are 18 to 28 nucleotides in length.
  • the shorter immunomodulating polynucleotides of the invention may retain immunomodulating activity of the longer, typical CpG ODNs and may exhibit higher immunomodulating activity (e.g., as measured by NF ⁇ B activation or by the changes in the expression levels of at least one cytokine (e.g., IL-6 or IL-10), as compared to longer CpG ODNs.
  • the shorter immunomodulating polynucleotides are easier and more economical to prepare, as their synthesis would involve fewer polynucleotide synthesis steps than the synthesis of a full length, typical CpG ODN.
  • the immunomodulating polynucleotides may contain one or more abasic spacers and/or internucleoside phosphotriesters.
  • the immunomodulating polynucleotides of the invention may exhibit stability (e.g., stability against nucleases) that is superior to that of CpG ODNs containing mostly internucleoside phosphate (e.g., more than 50% of internucleoside phosphates) without substantially sacrificing their immunostimulating activity.
  • This effect can be achieved, e.g., by incorporating at least 50% (e.g., at least 70%) internucleoside phosphorothioates or phosphorodithioates or through the inclusion of internucleoside phosphotriesters and/or internucleoside abasic spacers.
  • Phosphotriesters and abasic spacers are also convenient for conjugation to a targeting moiety.
  • a polynucleotide of the invention can include 15 or fewer contiguous internucleoside phosphorothioates (e.g., 14 or fewer, 13 or fewer, 12 or fewer, 11 or fewer, or 10 or fewer contiguous internucleoside phosphorothioates).
  • an immunostimulating polynucleotide containing a total of from 12 to 16 nucleosides may contain 10 or fewer contiguous internucleoside phosphorothioates.
  • the immunostimulating polynucleotide of the invention can contain a total of 50 or fewer nucleosides (e.g., 30 or fewer, 28 or fewer, or 16 or fewer nucleosides).
  • the immunostimulating polynucleotide of the invention can contain a total of at least 6 nucleosides (e.g., 10 or more or 12 or more nucleosides).
  • the immunostimulating polynucleotide of the invention can contain a total of from 6 to 30 nucleosides (e.g., a total of from 6 to 28 nucleosides, a total of from 6 to 20 nucleosides, a total of from 6 to 16 nucleosides, a total of from 10 to 20 nucleosides, a total of from 10 to 16 nucleosides, a total of from 12 to 28 nucleosides, a total of from 12 to 20 nucleosides, or a total of from 12 to 16 nucleosides).
  • nucleosides e.g., a total of from 6 to 28 nucleosides, a total of from 6 to 20 nucleosides, a total of from 6 to 16 nucleosides, a total of from 10 to 20 nucleosides, a total of from 10 to 16 nucleosides, a total of from 12 to 28 nucleosides, a total of from 12 to 20
  • the immunostimulating polynucleotide the invention can include one or more phosphotriesters (e.g., internucleoside phosphotriesters) and/or phosphorothioates (e.g., from 1 to 6 or from 1 to 4), e.g., at one or both termini (e.g., within the six 5′-terminal nucleosides or the six 3′-terminal nucleosides).
  • phosphotriesters e.g., internucleoside phosphotriesters
  • phosphorothioates e.g., from 1 to 6 or from 1 to 4
  • the inclusion of one or more internucleoside phosphotriesters and/or phosphorothioates can enhance the stability of the polynucleotide by reducing the rate of exonuclease-mediated degradation.
  • the immunostimulating polynucleotide of the invention contains a phosphotriester or a terminal phosphodiester, where the phosphotriester or the terminal phosphodiester includes a linker bonded to a targeting moiety or a conjugating group and optionally to one or more (e.g., 1 to 6) auxiliary moieties.
  • the immunostimulating polynucleotide contains only one linker. In some embodiments, the immunostimulating polynucleotide contains only one conjugating group.
  • the polynucleotide of the invention can be a hybridized polynucleotide including a strand and its partial or whole complement.
  • the hybridized polynucleotides can have at least 6 complementary base pairings (e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23), up to the total number of the nucleotides present in the included shorter strand.
  • the hybridized portion of the hybridized polynucleotide may contain 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 base pairs.
  • Conjugates of the invention contain a targeting moiety and one or more immunomodulating (e.g., immunostimulating) polynucleotides (e.g., from 1 to 6 or from 1 to 4 (e.g., 1 or 2) immunomodulating (e.g., immunostimulating) polynucleotides).
  • each of the immunomodulating polynucleotides includes independently a linker.
  • a targeting moiety is covalently bonded to the linker.
  • the linker may be bonded to a nucleobase, abasic spacer, phosphate, phosphorothioate, or phosphorodithioate in the immunomodulating polynucleotide.
  • the cells targeted by the conjugates of the invention are professional APCs (e.g., B cells, pDCs, or macrophages).
  • the targeting moiety can be an antigen-binding moiety (e.g., an antibody or antigen-binding fragment thereof), a polypeptide, an aptamer, or a group including one or more small molecules (e.g., mannose).
  • a targeting moiety may be an antibody or an antibody fragment.
  • a conjugate of the invention can contain an antibody or an antibody fragment and one or more immunomodulating polynucleotides covalently linked to a Q-tag in the antibody or the antibody fragment.
  • the Q-tag may be N-terminal or C-terminal.
  • the Q-tag may be disposed in the heavy or light chain of the antibody or the antibody fragment.
  • the use of targeting moiety-based delivery of the immunomodulating polynucleotides of the invention to specifically targeted tissues and cells may overcome the disadvantages of the typically uneven distribution of immunomodulating polynucleotides in vivo.
  • the targeting moiety-based delivery of the immunomodulating polynucleotides of the invention may be advantageous to systemic administration or to administration to a target tissue of immunomodulating polynucleotides, as systemic administration and the administration to a target tissue may produce an undesirable distribution of the immunomodulating polynucleotides through blood circulation in vivo, whereas a conjugate of the invention may undergo the intracellular delivery predominantly at the target tissue or cells, even when systemically administered.
  • the distribution-related advantages may be particularly pronounced in conjugates containing short immunomodulating polynucleotide(s) (e.g., immunomodulating polynucleotides containing a total of 6 to 16 nucleosides (e.g., a total of 10 to 16 or 12 to 16 nucleosides)).
  • immunomodulating polynucleotide(s) e.g., immunomodulating polynucleotides containing a total of 6 to 16 nucleosides (e.g., a total of 10 to 16 or 12 to 16 nucleosides)).
  • the conjugates of the invention may further contain one or more (e.g., from 1 to 6) auxiliary moieties (e.g., polyethylene glycols (PEGs)).
  • the auxiliary moiety may be a part of a capping group, bioreversible group, or non-bioreversible group.
  • the auxiliary moieties may be bonded to the linkers (e.g., to the linkers bonded to phosphates, phosphorothioates, or phosphorodithioates in the immunomodulating (e.g., immunostimulating) polynucleotides).
  • Inclusion of the auxiliary moieties (e.g., PEGs) in the conjugates of the invention may improve pharmacokinetic and/or biodistribution properties of the conjugates relative to a reference conjugate lacking such auxiliary moieties.
  • One or more of the immunomodulating polynucleotides of the invention can be conjugated to a targeting moiety (e.g., an antigen-binding moiety) that targets an antigen-presenting cell (APC; e.g., a professional APC (e.g., B-cell, pDC, or macrophage)).
  • a targeting moiety e.g., an antigen-binding moiety
  • APC antigen-presenting cell
  • an antigen-presenting cell e.g., a professional APC (e.g., B-cell, pDC, or macrophage)
  • an endosomal toll-like receptor e.g., TLR9
  • APC antigen-presenting cell
  • TLR9 endosomal toll-like receptor
  • activation of an endosomal toll-like receptor can induce proinflammatory cytokines (e.g., IL-6, IL-10, and/or type I interferon); this activity is believed to be useful for the treatment of various tumors (e.g., solid and liquid tumors in a patient).
  • cytokines e.g., IL-6, IL-10, and/or type I interferon
  • each X N is independently a nucleotide
  • X 3′ is a 3′ terminal nucleotide
  • X 5′ is a 5′ terminal nucleotide
  • Y P is an internucleoside phosphotriester
  • b and c are each an integer ranging from about 0 to about 25; with the proviso that their sum is no less than 5;
  • oligonucleotide comprises a nucleotide with a modified nucleobase.
  • b is an integer ranging from about 1 to about 15. In certain embodiments, b is an integer of about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, or about 15. In certain embodiments, b is an integer of about 3, about 4, about 11, or about 14. In certain embodiments, b is an integer of about 3. In certain embodiments, b is an integer of about 4. In certain embodiments, b is an integer of about 11. In certain embodiments, b is an integer of about 14.
  • c is an integer ranging from about 0 to about 10. In certain embodiments, c is an integer of about 0, about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, or about 10. In certain embodiments, c is an integer of about 0 or about 8. In certain embodiments, c is an integer of about 0. In certain embodiments, c is an integer of about 8.
  • b is an integer of about 3 and c is an integer of about 8. In certain embodiments, b is an integer of about 4 and c is an integer of about 8. In certain embodiments, b is an integer of about 11 and c is an integer of about 0. In certain embodiments, b is an integer of about 14 and c is an integer of about 0.
  • b and c together in total are ranging from about 5 to about 20. In certain embodiments, b and c together in total ranging from about 5 to about 15. In certain embodiments, b and c together in total are about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, or about 15. In certain embodiments, b and c together in total are about 8, about 9, about 10, about 11, about 12, about 13, or about 14. In certain embodiments, b and c together in total are about 11. In certain embodiments, b and c together in total are about 12. In certain embodiments, b and c together in total are about 14.
  • each X N is independently a 2′-deoxyribonucleotide or a 23-modified ribonucleotide.
  • each X N is independently 2′-deoxyadenosine (A), 23-deoxyguanosine (G), 2′-deoxycytidine (C), a 5-halo-2′-deoxycytidine, 2′-deoxythymidine (T), 23-deoxyuridine (U), a 5-halo-2′-deoxyuridine, a 2′-fluororibonucleotide, a 2′-methoxyribonucleotide, or a 23-(2-methoxyethoxy)ribonucleotide.
  • each X N is independently a 23-deoxyribonucleotide. In certain embodiments, each X N is independently 2′-deoxyadenosine, 23-deoxyguanosine, 2′-deoxycytidine, a 5-halo-2′-deoxycytidine, 2′-deoxythymidine, 2′-deoxyuridine, or a 5-halo-2′-deoxyuridine.
  • each X N is each X N is independently 2′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxycytidine, 2′-deoxythymidine, 5-bromo-2′-deoxyuridine, or 5-iodo-2′-deoxyuridine.
  • X 3′ is a 2′-deoxyribonucleotide or a 2′-modified ribonucleotide. In certain embodiments, X 3′ is a 2′-deoxyribonucleotide.
  • X 3′ is 2′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxycytidine, a 5-halo-2′-deoxycytidine, 2′-deoxythymidine, 2′-deoxyuridine, a 5-halo-2′-deoxyuridine, a 2′-fluororibonucleotide, a 2′-methoxyribonucleotide, or a 2′-(2-methoxyethoxy)ribonucleotide.
  • X 3′ is 2′-deoxyadenosine, 2′-deoxyguanosine, 23-deoxycytidine, a 5-halo-2′-deoxycytidine, 2′-deoxythymidine, 2′-deoxyuridine, or a 5-halo-2′-deoxyuridine.
  • X 3′ is 2′-deoxythymidine.
  • X 3′ is a 2′-deoxyribonucleotide with a substituted pyrimidine base.
  • X 3′ is a 2′-deoxyribonucleotide with a 5-substituted pyrimidine base.
  • X 3′ is 2′-deoxythymidine, a 5-halo-2′-deoxycytidine, or a 5-halo-2′-deoxyuridine. In certain embodiments, X 3′ is 2′-deoxythymidine, 5-bromo-2′-deoxycytidine, 5-iodo-2′-deoxycytidine, 5-bromo-2′-deoxyuridine, or 5-iodo-2′-deoxyuridine. In certain embodiments, X 3′ is 2′-deoxythymidine, 5-bromo-2′-deoxyuridine, or 5-iodo-2′-deoxyuridine.
  • X 3′ is a terminal nucleotide comprising a 3′ capping group.
  • the 3′ capping group is a terminal phosphoester.
  • the 3′ capping group is 3-hydroxyl-propylphosphoryl (i.e., —P(O 2 )—CH 2 CH 2 CH 2 OH).
  • X 5′ is a 2′-deoxyribonucleotide or a 2′-modified ribonucleotide. In certain embodiments, X 5′ is a 2′-deoxyribonucleotide.
  • X 5′ is 2′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxycytidine, a 5-halo-2′-deoxycytidine, 2′-deoxythymidine, 2′-deoxyuridine, a 5-halo-2′-deoxyuridine, a 2′-fluororibonucleotide, a 2′-methoxyribonucleotide, or a 2′-(2-methoxyethoxy)ribonucleotide.
  • X 5′ is 2′-deoxyadenosine, 2′-deoxyguanosine, 23-deoxycytidine, a 5-halo-2′-deoxycytidine, 2′-deoxythymidine, 2′-deoxyuridine, or a 5-halo-2′-deoxyuridine.
  • X 5′ is a 2′-deoxyribonucleotide with a substituted pyrimidine base.
  • X 5′ is a 2′-deoxyribonucleotide with a 5-substituted pyrimidine base.
  • X 5′ is 2′-deoxythymidine, a 5-halo-2′-deoxycytidine, or a 5-halo-2′-deoxyuridine. In certain embodiments, X 5′ is a 5-halo-2′-deoxycytidine. In certain embodiments, X 5′ is a 5-halo-2′-deoxyuridine. In certain embodiments, X 5′ is 2′-deoxythymidine, 5-bromo-2′-deoxycytidine, 5-iodo-2′-deoxycytidine, 5-bromo-2′-deoxyuridine, or 5-iodo-2′-deoxyuridine.
  • X 5′ is 2′-deoxythymidine, 5-bromo-2′-deoxyuridine, or 5-iodo-2′-deoxyuridine. In certain embodiments, X 5′ is 5-bromo-2′-deoxyuridine. In certain embodiments, X 5′ is 5-iodo-2′-deoxyuridine. In certain embodiments, X 5′ has a 3′-phosphorothoate group. In certain embodiments, X 5′ has a 3′-phosphorothoate group with a chirality of Rp. In certain embodiments, X 5′ has a 3′-phosphorothoate group with a chirality of Sp.
  • Y P is an internucleoside phosphothiotriester.
  • Y P is:
  • Z is O or S; and d is an integer ranging from about 0 to about 50.
  • Z is O.
  • Z is S.
  • d is an integer ranging from about 0 to about 10.
  • d is an integer ranging from about 0 to about 5.
  • d is an integer of about 0, about 1, about 2, about 3, about 4, or about 5.
  • d is an integer of about 0, about 1, or about 3.
  • Y P is:
  • Z is O or S; and d is an integer ranging from about 0 to about 50.
  • Z is O.
  • Z is S.
  • d is an integer ranging from about 0 to about 10.
  • d is an integer ranging from about 0 to about 5.
  • d is an integer of about 0, about 1, about 2, about 3, about 4, or about 5.
  • d is an integer of about 0, about 1, or about 3.
  • the oligonucleotide of Formula (A) comprises one additional internucleoside phosphotriester.
  • the additional internucleoside phosphotriester is a C 1-6 alkylphosphotriester.
  • the additional internucleoside phosphotriester is ethylphosphotriester.
  • the oligonucleotide of Formula (A) comprises one 5-halo-2′-deoxyuridine.
  • the 5-halo-2′-deoxyuridine is 5-fluoro-2′-deoxyuridine, 5-bromo-2′-deoxyuridine, or 5-iodo-2′-deoxyuridine.
  • the 5-halo-2′-deoxyuridine is 5-bromo-2′-deoxyuridine or 5-iodo-2′-deoxyuridine.
  • the 5-halo-2′-deoxyuridine is 5-fluoro-2′-deoxyuridine.
  • the 5-halo-2′-deoxyuridine is 5-bromo-2′-deoxyuridine.
  • the 5-halo-2′-deoxyuridine is 5-iodo-2′-deoxyuridine.
  • the oligonucleotide of Formula (A) comprises three or more 2′-deoxycytidines. In certain embodiments, the oligonucleotide of Formula (A) comprises three 23-deoxycytidines.
  • the oligonucleotide of Formula (A) comprises four or more 2′-deoxyguanosines. In certain embodiments, the oligonucleotide of Formula (A) comprises four 2′-deoxyguanosines.
  • the oligonucleotide of Formula (A) comprises three 2′-deoxycytidines and four 2′-deoxyguanosines. In certain embodiments, the oligonucleotide of Formula (A) comprises one, two, or three CG dinucleotides. In certain embodiments, the oligonucleotide of Formula (A) comprises three CG dinucleotides.
  • the oligonucleotide of Formula (A) comprises three or more 2′-deoxythymidines. In certain embodiments, the oligonucleotide of Formula (A) comprises three, four, five, six, seven, or eight 2′-deoxythymidines. In certain embodiments, the oligonucleotide of Formula (A) comprises three, four, five, or eight 2′-deoxythymidines.
  • the oligonucleotide of Formula (A) does not comprise a 23-deoxyadenosine. In certain embodiments, the oligonucleotide of Formula (A) comprises one or two 23-deoxyadenosines.
  • the oligonucleotide of Formula (A) has a length ranging from about 5 to about 20 or from about 6 to about 15 nucleotides. In certain embodiments, the oligonucleotide of Formula (A) has a length of about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, or about 15. In certain embodiments, the oligonucleotide of Formula (A) has a length of about 10, about 11, about 12, about 13, about 14, or about 15.
  • the oligonucleotide of Formula (A) comprises one or more internucleoside phosphorothioates. In certain embodiments, all the internucleoside phosphoesters in the oligonucleotide of Formula (A) are internucleoside phosphorothioates. In certain embodiments, the oligonucleotide of Formula (A) comprises one or more chiral internucleoside phosphorothioates.
  • the oligonucleotide of Formula (A) is p275, p276, p313, or p347. In certain embodiments, the oligonucleotide of Formula (A) is p236, p238, p243, p246, p308, p361, p362, or p425.
  • the oligonucleotide of Formula (A) is p236, p238, p243, p246, p275, p276, p308, p313, p347, p361, p362, p425, p433, p434, p435, p436, p437, p438, p477, p478, p479, p480, p481, p482, p483, p484, p485, p486, p487, p488, or p489.
  • the oligonucleotide of Formula (A) is an immunomodulating oligonucleotide.
  • an oligonucleotide having a sequence of N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), or a stereoisomer, a mixture of two or more diastereomers, a tautomer, or a mixture of two or more tautomers thereof; or a pharmaceutically acceptable salt, solvate, or hydrate thereof; wherein:
  • x is an integer ranging from 1 to 4.
  • N 1 is absent or 2′-deoxythymidine
  • N 2 is a 2′-deoxyribonucleotide with a modified nucleobase
  • N 3 is 2′-deoxyadenosine or 2′-deoxythymidine, each optionally comprising a 3′-phosphotriester;
  • N 4 is 2′-deoxyadenosine or 2′-deoxythymidine
  • N 5 is 2′-deoxythymidine optionally comprising a 3′-phosphotriester
  • C is 2′-deoxycytidine and G is 2′-deoxyguanosine.
  • x is an integer of 1, 2, 3, or 4. In certain embodiments, in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), x is an integer of 1. In certain embodiments, in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), x is an integer of 4.
  • N 1 is absent. In certain embodiments, in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), N 1 is 2′-deoxythymidine.
  • N 2 in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), N 2 is a 2′-deoxyribonucleotide with a substituted pyrimidine base. In certain embodiments, in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), N 2 is a 2′-deoxyribonucleotide with a 5-substituted pyrimidine base.
  • N 2 in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), N 2 is a 5-halo-2′-deoxycytidine or a 5-halo-2′-deoxyuridine. In certain embodiments, in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), N 2 is 5-bromo-2′-deoxyuridine or 5-iodo-2′-deoxyuridine.
  • N 3 is 2′-deoxyadenosine comprising a 3′-phosphotriester. In certain embodiments, in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), N 3 is 2′-deoxythymidine. In certain embodiments, in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), N 3 is 2′-deoxythymidine comprising a 3′-phosphotriester.
  • N 4 is 2′-deoxyadenosine. In certain embodiments, in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), N 4 is 2′-deoxythymidine.
  • N 5 is 2′-deoxythymidine in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497). In certain embodiments, in N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497), N 5 is 2′-deoxythymidine comprising a 3′-phosphotriester.
  • the oligonucleotide of N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T comprises one or more internucleoside phosphorothioates. In certain embodiments, the oligonucleotide of N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497) comprises at least one chiral internucleoside phosphorothioates.
  • the oligonucleotide of N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497) is p275, p276, or p313. In certain embodiments, the oligonucleotide of N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497) is p236, p238, p243, p246, p308, p361, p362, or p425.
  • the oligonucleotide of N 1 N 2 CGN 3 CG(T) x GN 4 CGN 5 T(SEQ ID NO: 497) is p236, p238, p243, p246, p275, p276, p308, p313, p347, p361, p362, p425, p433, p434, p435, p436, p437, p438, p477, p478, p479, p480, p481, p482, p483, p484, p485, p486, p487, p488, or p489.
  • Immunostimulating polynucleotides of the invention can function as PAMPs and can activate innate immune response or stimulate adaptive immune response by triggering TLR9 signaling (e.g., as TLR9 agonists).
  • TLR9 signaling e.g., as TLR9 agonists.
  • the sequences that may be used in the immunostimulating polynucleotides of the invention are those known in the art for class B CpG polynucleotides, or their modifications including 5-halouridine or 5-alkynyluridine, or truncated versions thereof (e.g., those containing a total of 6 to 16 nucleosides).
  • the truncated immunostimulating polynucleotides of the invention may contain a truncated class B CpG polynucleotide sequence (e.g., a class B CpG polynucleotide sequence, from which one or more 3′-terminal nucleotides are eliminated or one or more of the intra-sequence nucleotides excised).
  • a truncated class B CpG polynucleotide sequence e.g., a class B CpG polynucleotide sequence, from which one or more 3′-terminal nucleotides are eliminated or one or more of the intra-sequence nucleotides excised.
  • the immunostimulating polynucleotide of the invention contains at least one immunostimulating sequence (ISS).
  • an immunostimulating polynucleotide of the invention can contain 1, 2, 3 or 4 ISS.
  • the ISS in immunostimulating polynucleotides is dependent on the targeted organism.
  • the common feature of the ISS used in the immunostimulating polynucleotides of the invention is the cytidine-p-guanosine sequence, in which p is an internucleoside phosphodiester (e.g., phosphate or phosphorothioate) or an internucleoside phosphotriester.
  • cytidine and guanosine in the ISS contain 2′-deoxyribose.
  • the immunostimulating polynucleotide of the invention contains 1, 2, or 3 human ISSs.
  • the human ISS can be CG or NCG, where N is uridine, cytidine, or thymidine, or a modified version of uridine or cytidine, as disclosed herein (e.g., a 5-halouridine (e.g., 5-iodouridine or 5-bromouridine), a 5-alkynyluridine (e.g., 5-ethynyluridine or 5-propynyluridine), 5-heteroaryluridine, or 5-halocytidine); and G is guanosine or a modified version thereof, as disclosed herein (e.g., 7-deazaguanosine).
  • a 5-halouridine e.g., 5-iodouridine or 5-bromouridine
  • a 5-alkynyluridine e.g., 5-ethynyluridine or 5-propyn
  • the human ISS is NCG (e.g., where N is 5-halouridine).
  • the human ISS is UCG (e.g., where U is 5-alkynyluridine (e.g., 5-ethynyluridine)).
  • an immunostimulating polynucleotide of the invention targeting humans contains an ISS within four contiguous nucleotides that include a 5′-terminal nucleotide (e.g., an immunostimulating polynucleotide of the invention contains a 5′-terminal ISS).
  • Murine ISS is a hexameric nucleotide sequence: Pu-Pu-CG-Py-Py, where each Pu is independently a purine nucleotide, and each Py is independently a pyrimidine nucleotide.
  • the 5′-flanking nucleotides relative to CpG in the immunostimulating polynucleotides of the invention does not contain 2′-alkoxyriboses.
  • the 5′-flanking nucleotides relative to CpG in the immunostimulating polynucleotides of the invention contains only 2′-deoxyriboses as sugars.
  • the structural features of the immunostimulating polynucleotides of the invention may include: (1) high content of phosphorothioates (e.g., at least 50%, at least 60%, at least 70%, or at least 80% of nucleosides may be linked by phosphorothioates), (2) absence of poly-G tails, (3) nucleosides in the immunostimulating polynucleotides may contain 2′-deoxyriboses or 2′-modified riboses (e.g., 2′-halo (e.g., 2′-fluoro) or optionally substituted 2′-alkoxy (e.g., 2′-methoxy)), and/or (4) the inclusion of 5′-terminal ISS that is NCG, in which N is uridine, cytidine, or thymidine, or a modified version of uridine or cytidine, as disclosed herein (e.g., a 5-halouridine (e.g., 5-iod
  • the conjugate contains one targeting moiety (e.g., an antibody or antigen-binding fragment thereof) and one immunomodulating polynucleotide covalently linked to the targeting moiety.
  • one targeting moiety e.g., an antibody or antigen-binding fragment thereof
  • one immunomodulating polynucleotide covalently linked to the targeting moiety.
  • immunosuppressive polynucleotides of the invention can suppress adaptive immune response by reducing activation of TLR9 signaling (e.g., through TLR9 antagonism).
  • immunosuppressive polynucleotides of the invention include at least two 2′-alkoxynucleotides that are 5′-flanking relative to CpG, as described by the following formula: N 1 —N 2 —CG, where each of N 1 and N 2 is independently a nucleotide containing 2′-alkoxyribose (e.g., 2′-methoxyribose).
  • the immunomodulating polynucleotides disclosed herein may include one or more (e.g., one or two) abasic spacers (e.g., internucleoside abasic spacers and/or terminal abasic spacers).
  • abasic spacers e.g., internucleoside abasic spacers and/or terminal abasic spacers.
  • the structures of the abasic spacers may be same or different.
  • An abasic spacer is of formula (I): R 1 -L 1 -[-L 2 -(L 1 ) n1 -] n2 -R 2 , (I)
  • n1 0 or 1
  • n2 is an integer from 1 to 6
  • R 1 is a bond to a nucleoside in the immunomodulating polynucleotide
  • R 2 is a bond to a nucleoside in the immunomodulating polynucleotide or to a capping group
  • each L 1 is independently a phosphodiester or a phosphotriester
  • each L 2 is a sugar analogue.
  • abasic spacer is an internucleoside, abasic spacer, n1 is 1, and R 2 is a bond to a nucleoside, and if the abasic spacer is a terminal, abasic spacer, n1 is 0 or 1, and R 2 is a bond to a capping group.
  • the abasic spacer is an internucleoside, abasic spacer or a 3′-terminal, abasic spacer.
  • each two contiguous L 2 groups are separated by L 1 groups (e.g., n1 is 1 for L 1 disposed between two contiguous L 2 groups).
  • the immunostimulating polynucleotide contains an ISS disposed within four contiguous nucleotides that include a 5′-terminal nucleotide of the immunostimulating polynucleotide,
  • the ISS is NCG, where N is uridine, cytidine, or thymidine, or a modified version of uridine orcytidine, as disclosed herein (e.g., a 5-halouridine (e.g., 5-iodouridine or 5-bromouridine), a 5-alkynyluridine (e.g., 5-ethynyluridine or 5-propynyluridine), 5-heteroaryluridine, or 5-halocytidine), and
  • N and C are linked to each other through a phosphodiester or phosphotriester.
  • a sugar analogue is a divalent or trivalent group that is a C 3-6 monosaccharide or C 3-6 alditol (e.g., glycerol), which is modified to replace two hydroxyl groups with bonds (i) to an oxygen atom in one phosphoester and (ii) to an oxygen atom in another phosphoester or to a capping group.
  • a sugar analogue is cyclic or acyclic.
  • Non-limiting examples of sugar analogues are optionally substituted C 2-6 alkylene, optionally substituted C 2-6 alkenylene, optionally substituted C 5 cycloalkane-1,3-diyl, optionally substituted C 5 cycloalkene-1,3-diyl, optionally substituted heterocycle-1,3-diyl (e.g., optionally substituted pyrrolidine-2,5-diyl, optionally substituted tetrahydrofuran-2,5-diyl, or optionally substituted tetrahydrothiophene-2,5-diyl), or optionally substituted (C 1-4 alkyl)-(C 3-8 cycloalkylene) (e.g., optionally substituted (C 1 alkyl)-(C 3 cycloalkylene)).
  • Non-limiting examples of sugar analogues are:
  • each of R 1 and R 2 is independently a bond to an oxygen atom in a phosphoester
  • each of R 3 and R 4 is independently H; optionally substituted C 1-6 alkyl; —(CH 2 ) t1 —OR Z ; or -LinkA-R T ;
  • t1 is an integer from 1 to 6;
  • R Z is optionally substituted C 1-6 alkyl, optionally substituted C 2-6 alkenyl, optionally substituted C 2-6 alkynyl, optionally substituted C 6-14 aryl, optionally substituted C 3-8 cycloalkyl, optionally substituted (C 1-9 heterocyclyl)-C 1-6 -alkyl, optionally substituted (C 6-10 aryl)-C 1-6 -alkyl, optionally substituted (C 3-8 cycloalkyl)-C 1-6 -alkyl;
  • LinkA is linker
  • R T is a bond to a targeting moiety; a conjugation moiety; optionally substituted C 1-6 alkyl, optionally substituted C 2-6 alkenyl, optionally substituted C 2-6 alkynyl, optionally substituted C 6-14 aryl, optionally substituted C 3-8 cycloalkyl, optionally substituted (C 1-9 heterocyclyl)-C 1-6 -alkyl, optionally substituted (C 6-10 aryl)-C 1-6 -alkyl, or optionally substituted (C 3-8 cycloalkyl)-C 1-6 -alkyl.
  • R Z is optionally substituted C 1-6 aminoalkyl (e.g., optionally substituted C 1-6 amino alkyl containing —NH 2 ).
  • the immunomodulating polynucleotides of the invention may contain one or more internucleoside phosphotriesters and/or one or two terminal phosphodiesters and/or phosphotriesters.
  • a phosphotriester may contain a phosphate, phosphorothioate, or phosphorodithioate, in which one or two valencies are substituted with nucleosides and/or abasic spacers, and the remaining valencies are bonded to a bioreversible group, a non-bioreversible group, a linker bonded to a targeting moiety, or a conjugating group.
  • An internucleoside phosphotriester is bonded to two nucleosides and/or abasic spacers, and the remaining valency is bonded to a bioreversible group, a non-bioreversible group, a linker bonded to a targeting moiety, or a conjugating group.
  • An internucleoside phosphodiester is bonded to two nucleosides and/or abasic spacers.
  • a terminal phosphodiester contains a phosphate, phosphorothioate, or phosphorodithioate at the 5′- or 3′-terminus of the immunomodulating polynucleotide, where one of the two remaining valencies is bonded to a bioreversible group, a non-bioreversible group, a linker bonded to a targeting moiety, or a conjugating group.
  • the immunomodulating polynucleotides of the invention may contain a linker bonded to a targeting moiety and optionally one or more auxiliary moieties.
  • the linker has a molecular weight of from 43 Da to 10 kDa (e.g., from 100 Da to 8 kDa, from 100 Da to 7 kDa, or from 100 Da to 3 kDa).
  • the linker may be represented herein as LinkA.
  • the linker may be a multivalent group, in which the first valency is bonded to an internucleoside or terminal phosphate, an internucleoside or terminal phosphorothioate, an internucleoside or terminal phosphorodithioate, an abasic spacer, a capping group, or a nucleobase, and a second valency is bonded to a targeting moiety.
  • the linker may further include one or more valencies, each of which is independently bonded to an auxiliary moiety.
  • the immunomodulating polynucleotide contains multiple linkers to multiple targeting moieties.
  • the immunomodulating polynucleotide may contain one linker to a targeting moiety.
  • the immunomodulating polynucleotides disclosed herein may include a conjugating group.
  • a conjugating group includes at least one conjugationg moiety which is a functional group that is capable of undergoing a conjugation reaction (e.g., a cycloaddition reaction (e.g., dipolar cycloaddition), amidation reaction, or nucleophilic aromatic substitution) or is rendered capable of undergoing a conjugation reaction, upon deprotection of the functional group.
  • a conjugation reaction e.g., a cycloaddition reaction (e.g., dipolar cycloaddition), amidation reaction, or nucleophilic aromatic substitution
  • the conjugating group Upon reaction with a complementary reactive group, the conjugating group produces the linker in the immunomodulating polynucleotide of the invention.
  • the linker bonded to a targeting moiety is part of an internucleoside phosphotriester. In certain embodiments, the linker bonded to a targeting moiety is part of an abasic spacer.
  • the linker e.g., LinkA
  • a conjugating group is of formula (II): —Z 1 -Q A1 -Z 2 -(-Q A2 -Z 3 —) k —R T , (II)
  • Z 1 is a divalent group, a trivalent group, a tetravalent group, or a pentavalent group, in which one of valency is bonded to Q A1 , the second valency is open or, if formula (II) is for the linker, is bonded to R T , and each of the remaining valencies, when present, is independently bonded to an auxiliary moiety;
  • Z 2 is absent, a divalent group, a trivalent group, a tetravalent group, or a pentavalent group, in which one of valency is bonded to Q A1 , the second valency is bonded to Q A2 or R T , and each of the remaining valencies, when present, is independently bonded to an auxiliary moiety;
  • Z 3 is absent, a divalent group, a trivalent group, a tetravalent group, or a pentavalent group, in which one of valency is bonded to Q A2 , the second valency is bonded to R T , and each of the remaining valencies, when present, is independently bonded to an auxiliary moiety;
  • R T is absent or a bond to a targeting moiety
  • k 0 or 1.
  • Q A1 and Q A2 is independently absent, optionally substituted C 2-12 heteroalkylene (e.g., a heteroalkylene containing —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —), optionally substituted C 1-12 thioheterocyclylene
  • C 1-12 heterocyclylene e.g., 1,2,3-triazole-1,4-diyl or
  • R T is a bond to a targeting moiety
  • Q A2 is absent, and Q A1 is a conjugation moiety, e.g., optionally substituted C 2-12 alkynyl, optionally substituted N-protected amino, azido, N-maleimido, S-protected thiol,
  • 1,2,4,5-tetrazine group e.g., 1,2,4,5-tetrazine group
  • Q A1 is as defined for the linker, and Q A2 is a conjugation moiety, e.g., optionally substituted C 2-12 alkynyl, optionally substituted N-protected amino, azido, N-maleimido, S-protected thiol,
  • R N1 is H, N-protecting group, or optionally substituted C 1-6 alkyl
  • each R 12 is independently H or optionally substituted C 1-6 alkyl
  • R 13 is halogen (e.g., F);
  • Z 1 has a branching group and two divalent segments, where the branching group is bonded to each of the two divalent segments,
  • one of the divalent segments is bonded to an internucleoside or terminal phosphate, an internucleoside or terminal phosphorothioate, an internucleoside or terminal phosphorodithioate, an abasic spacer, or a nucleobase, and the remaining divalent segment is bonded to Q A1 ;
  • the branching group is optionally substituted C 1-12 alkane-triyl or optionally substituted C 2-12 heteroalkane-triyl, in which two valencies are substituted with the divalent segments, and the remaining valency is substituted with
  • Z 2 has a branching group and two divalent segments, where the branching group is bonded to each of the two divalent segments,
  • one of the divalent segments is bonded to a targeting moiety or Q A2 , and the remaining divalent segment is bonded to Q A1 ;
  • the branching group is optionally substituted C 1-12 alkane-triyl or optionally substituted C 2-12 heteroalkane-triyl, in which two valencies are substituted with the divalent segments, and the remaining valency is substituted with
  • Z 3 has a branching group and two divalent segments, where the branching group is bonded to each of the two divalent segments,
  • one of the divalent segments is bonded to a targeting moiety, and the remaining divalent segment is bonded to Q A2 ;
  • the branching group is optionally substituted C 1-12 alkane-triyl or optionally substituted C 2-12 heteroalkane-triyl, in which two valencies are substituted with the divalent segments, and the remaining valency is substituted with
  • the divalent segment in Z 1 , Z 2 , or Z 3 may be -(-Q B -Q C -Q D -) s1 -,
  • each s1 is independently an integer from 1 to 50 (e.g., from 1 to 30);
  • each Q B and each Q D is independently absent, —CO—, —NH—, —O—, —S—, —SO 2 —, —OC(O)—, —COO—, —NHC(O)—, —C(O)NH—, —CH 2 —, —CH 2 NH—, —NHCH 2 —, —CH 2 O—, or —OCH 2 —; and
  • each Q C is independently absent, optionally substituted C 1-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, optionally substituted C 2-12 heteroalkylene, or optionally substituted C 1-9 heterocyclylene;
  • At least one Q C is present in the divalent segment.
  • Q C is present in each monomeric unit of the divalent segment.
  • Z 1 is bonded through a Q C that is present.
  • at least one of Q B and Q D is present in each monomeric unit of Z 1 .
  • at least one of Q B and Q D is present in each monomeric unit of Z 2 .
  • only one of Z 1 , Z 2 , and Z 3 when present, contains a branching group.
  • one, two, or three of Z 1 , Z 2 , and Z 3 are independently -(-Q B -Q C -Q D -) s1 -Q E -(-Q B -Q C -Q D -) s1 -, (III)
  • each s1 is independently an integer from 1 to 50 (e.g., from 1 to 30);
  • each Q B and each Q D is independently absent, —CO—, —NH—, —O—, —S—, —SO 2 —, —OC(O)—, —COO—, —NHC(O)—, —C(O)NH—, —CH 2 —, —CH 2 NH—, —NHCH 2 —, —CH 2 O—, or —OCH 2 —; and
  • each Q C is independently absent, optionally substituted C 1-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, optionally substituted C 2-12 heteroalkylene, optionally substituted C 1-9 heterocyclylene, or —P(Z)(OH)—, where Z is O or S; and
  • Q G is absent, if p1 is 1; and at least one Q G is present, if p1 is 2 or 3.
  • Z 1 is bonded to an internucleoside or terminal phosphate, an internucleoside or terminal phosphorothioate, an internucleoside or terminal phosphorodithioate, an abasic spacer, a capping group, or a nucleobase through a Q C that is present.
  • each Q B and each Q D is independently absent, —CO—, —NH—, —O—, —S—, —SO 2 —, —NHC(O)—, —C(O)NH—, —CH 2 —, —CH 2 NH—, —NHCH 2 —, —CH 2 O—, or —OCH 2 —.
  • -(-Q B -Q C -Q D -) s1 - combine to form a group: -Q B -(CH 2 ) g1 —(CH 2 OCH 2 ) g2 —(CH 2 ) g3 -Q D -,
  • g2 is an integer from 1 to 50;
  • g1 is 1 and Q B is —NHCO—, —CONH—, or —O—; or g1 is 0 and Q D is —NHCO—;
  • g3 is 1 and Q B is —NHCO—, —CONH—, or —O—; or g3 is 0 and Q D is —CONH—.
  • the conjugation moiety may be protected until an auxiliary moiety is conjugated to the polynucleotide.
  • a conjugation moiety that is protected may include —COOR PGO or —NHR PGN , where R PGO is an O-protecting group (e.g., a carboxyl protecting group), and R PGN is an N-protecting group.
  • Link A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • each of Q A1 and Q A2 is absent, independently optionally substituted C 2-12 heteroalkylene (e.g., a heteroalkylene containing —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —), optionally substituted C 1-12 thioheterocyclylene
  • C 2-12 heteroalkylene e.g., a heteroalkylene containing —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —
  • C 1-12 heterocyclylene e.g., 1,2,3-triazole-1,4-diyl or
  • R T is a bond to a targeting moiety
  • R P is a bond to an internucleoside bridging group, a nucleobase, a capping group, or an abasic spacer
  • Q T is —CO—, —NH—, —NH—CH 2 —, or —CO—CH 2 —;
  • each Q S is independently optionally substituted C 2-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, or optionally substituted (C 6-10 aryl)-C 1-6 -alkylene;
  • each R M is independently H, auxiliary moiety, —(CH 2 ) q7 —CO—N(R M1 ) 2 , or —C[—CH 2 O—(CH 2 ) q7 —CO—N(R M1 ) 2 ] 3 , where each q7 is independently an integer from 1 to 5, and each R M1 is independently H or an auxiliary moiety;
  • each of X 1 , X 3 , and X 5 is independently absent, —O—, —NH—, —CH 2 —NH—, —C(O)—, —C(O)—NH—, —NH—C(O)—, —NH—C(O)—NH—, —O—C(O)—NH—, —NH—C(O)—O—, —CH 2 —NH—C(O)—NH—, —CH 2 —O—C(O)—NH—, or —CH 2 —NH—C(O)—O—;
  • X 7 is absent, —O—, —O—P(O)(OH)—O—, —O—P(S)(OH)—O—, —NH—, —CH 2 —NH—, —C(O)—, —C(O)—NH—, —NH—C(O)—, —NH—C(O)—NH—, —O—C(O)—NH—, —NH—C(O)—O—, —CH 2 —NH—C(O)—NH—, —CH 2 —O—C(O)—NH—, or —CH 2 —NH—C(O)—O—;
  • each of X 2 , X 4 , and X 6 is independently absent, —O—, —NH—, —C(O)—, —C(O)—NH—, —NH—C(O)—, —NH—C(O)—NH—, —O—C(O)—NH—, or —NH—C(O)—O—;
  • x1 and each x5 are independently 0 or 1;
  • each x2 is independently an integer from 0 to 50 (e.g., from 1 to 40 or from 1 to 30); each x3 is independently an integer from 1 to 11;
  • x4 is 0, 1, or 2;
  • each x6 is independently an integer from 0 to 10 (e.g., from 1 to 6), provided that the sum of both x6 is 12 or less.
  • LinkA is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Q A1 is optionally substituted C 2-12 heteroalkylene (e.g., a heteroalkylene containing —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —), optionally substituted C 1-12 thioheterocyclylene
  • C 1-12 heterocyclylene e.g., 1,2,3-triazole-1,4-diyl or
  • each R M1 is independently H or an auxiliary moiety
  • R T is a bond to a targeting moiety
  • R P is a bond to an internucleoside bridging group, a nucleobase, a capping group, or an abasic spacer
  • Q T is —CO—, —NH—, —NH—CH 2 —, or —CO—CH 2 —;
  • Q P is —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —;
  • each Q S is independently optionally substituted C 2-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, or optionally substituted (C 6-10 aryl)-C 1-6 -alkylene; each of q1, q3, and q7 is independently 0 or 1;
  • each of q2 and q8 is an integer from 0 to 50 (e.g., from 1 to 40 or from 1 to 30);
  • q4 is an integer from 0 to 10;
  • each of q5 and q6 is independently an integer from 1 to 10 (e.g., from 1 to 6);
  • q9 is an integer from 1 to 10.
  • LinkA is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • each R M1 is independently H or an auxiliary moiety
  • R T is a bond to a targeting moiety
  • R P is a bond to an internucleoside bridging group, a nucleobase, a capping group, or an abasic spacer
  • Q T is —CO—, —CO—CH 2 —, —NH—, or —NH—CH 2 —;
  • Q P is —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —;
  • each Q S is independently optionally substituted C 2-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, or optionally substituted (C 6-10 aryl)-C 1-6 -alkylene;
  • each of q1, q3, and q7 is independently 0 or 1;
  • each of q2 and q8 is an integer from 0 to 50 (e.g., from 1 to 40 or from 1 to 30);
  • q4 is an integer from 0 to 10;
  • each of q5 and q6 is independently an integer from 1 to 10 (e.g., from 1 to 6);
  • q9 is an integer from 1 to 10.
  • q5 is 0. In other embodiments, q5 is an integer from 2 to 6.
  • a conjugating group is:
  • Q A1 is independently optionally substituted C 2-12 heteroalkylene (e.g., a heteroalkylene containing —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —), optionally substituted C 1-12 thioheterocyclylene
  • C 1-12 heterocyclylene e.g., 1,2,3-triazole-1,4-diyl or
  • Q A2 is optionally substituted C 2-12 alkynyl, optionally substituted N-protected amino, azido, N-maleimido, S-protected thiol,
  • R N1 is H, N-protecting group, or optionally substituted C 1-6 alkyl
  • each R 12 is independently H or optionally substituted C 1-6 alkyl
  • R 13 is halogen (e.g., F);
  • R P is a bond to an internucleoside bridging group, a nucleobase, a capping group, or an abasic spacer
  • each Q S is independently optionally substituted C 2-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, or optionally substituted (C 6-10 aryl)-C 1-6 -alkylene;
  • each R M is independently H, auxiliary moiety, —(CH 2 ) q7 —CO—N(R M1 ) 2 , or —C[—CH 2 O—(CH 2 ) q7 —CO—N(R M1 ) 2 ] 3 , where each q7 is independently an integer from 1 to 5, and each R M1 is independently H or auxiliary moiety;
  • each of X 3 and X 5 is independently absent, —O—, —NH—, —CH 2 —NH—, —C(O)—, —C(O)—NH—, —NH—C(O)—, —NH—C(O)—NH—, —O—C(O)—NH—, —NH—C(O)—O—, —CH 2 —NH—C(O)—NH—, —CH 2 —O—C(O)—NH—, or —CH 2 —NH—C(O)—O—;
  • X 7 is absent, —O—, —O—P(O)(OH)—O—, —O—P(S)(OH)—O—, —NH—CH 2 —NH—, —C(O)—, —C(O)—NH—, —NH—C(O)—, —NH—C(O)—NH—, —O—C(O)—NH—, —NH—C(O)—O—, —CH 2 —NH—C(O)—NH—, —CH 2 —O—C(O)—NH—, or —CH 2 —NH—C(O)—O—;
  • each of X 2 , X 4 , and X 6 is independently absent, —O—, —NH—, —O—, —C(O)—, —C(O)—NH—, —NH—C(O)—, —NH—C(O)—NH—, —O—C(O)—NH—, or —NH—C(O)—O—;
  • x1 and each x5 are independently 0 or 1;
  • each x2 is independently an integer from 0 to 50 (e.g., from 1 to 40 or from 1 to 30);
  • each x3 is independently an integer from 1 to 11;
  • x4 is 0, 1, or 2;
  • each x6 is independently an integer from 0 to 10 (e.g., from 1 to 6), provided that the sum of both x6 is 12 or less.
  • a conjugating group is:
  • Q A1 is optionally substituted C 2-12 alkynyl, optionally substituted N-protected amino, azido, N-maleimido, S-protected thiol
  • R N1 is H, N-protecting group, or optionally substituted C 1-6 alkyl
  • each R 12 is independently H or optionally substituted C 1-6 alkyl
  • R 13 is halogen (e.g., F);
  • R P is a bond to an internucleoside bridging group, a nucleobase, a capping group, or an abasic spacer
  • each Q S is independently optionally substituted C 2-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, or optionally substituted (C 6-10 aryl)-C 1-6 -alkylene;
  • X 7 is absent, —O—, —NH—, —O—P(O)(OH)—O—, —O—P(S)(OH)—O—, —CH 2 —NH—, —C(O)—, —C(O)—NH—, —NH—C(O)—, —NH—C(O)—NH—, —O—C(O)—NH—, —NH—C(O)—O—, —CH 2 —NH—C(O)—NH—, —CH 2 —O—C(O)—NH—, or —CH 2 —NH—C(O)—O—;
  • X 6 is absent, —O—, —NH—, —O—, —C(O)—, —C(O)—NH—, —NH—C(O)—, —NH—C(O)—NH—, —O—C(O)—NH—, or —NH—C(O)—O—;
  • x1 is independently 0 or 1;
  • each x2 is independently an integer from 0 to 50 (e.g., from 1 to 40 or from 1 to 30);
  • each x3 is independently an integer from 1 to 11;
  • x4 is 0, 1, or 2.
  • a conjugating group is:
  • Q A1 is optionally substituted C 2-12 alkynyl, optionally substituted N-protected amino, azido, N-maleimido, S-protected thiol,
  • R N1 is H, N-protecting group, or optionally substituted C 1-6 alkyl
  • each R 12 is independently H or optionally substituted C 1-6 alkyl
  • R 13 is halogen (e.g., F);
  • R P is a bond to an internucleoside bridging group, a nucleobase, a capping group, or an abasic spacer
  • Q P is —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —;
  • each Q S is independently optionally substituted C 2-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, or optionally substituted (C 6-10 aryl)-C 1-6 -alkylene;
  • each of q1 and q3 is independently 0 or 1;
  • q2 is an integer from 0 to 50 (e.g., from 1 to 40 or from 1 to 30);
  • q4 is an integer from 0 to 10.
  • q5 is an integer from 1 to 10 (e.g., from 1 to 6).
  • the conjugating group is:
  • R P is a bond to an internucleoside bridging group, a nucleobase, a capping group, or an abasic spacer
  • Q P is —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —;
  • each Q S is independently optionally substituted C 2-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, or optionally substituted (C 6-10 aryl)-C 1-6 -alkylene;
  • each of q1 and q3 is independently 0 or 1;
  • q2 is an integer from 0 to 50 (e.g., from 1 to 40 or from 1 to 30);
  • q4 is an integer from 0 to 10.
  • q5 is an integer from 1 to 10 (e.g., from 1 to 6).
  • a conjugating group is:
  • q2 is an integer from 1 to 50 (e.g., an integer from 1 to 24 or from 1 to 8 (e.g., 2 or 3))
  • q4 is an integer from 0 to 10 (e.g., 0, 1, 2, 3, 4, 5, 6, 7, or 8)
  • q10 is an integer from 0 to 8 (e.g., 1, 2, 3, 4, 5, or 6)
  • q11 is 0 or 1
  • Z is O or S
  • each R M is independently H, auxiliary moiety, —(CH 2 ) q7 —CO—N(R M1 ) 2 , or —C[—CH 2 O—(CH 2 ) q7 —CO—N(R M1 ) 2 ] 3 , where each q7 is independently an integer from 1 to 5, and each R M1 is independently H or auxiliary moiety.
  • conjugating groups can be used for conjugation to a targeting moiety through a metal-catalyzed cycloaddition:
  • q2 is an integer from 1 to 50 (e.g., an integer from 1 to 24 or from 1 to 8 (e.g., 2 or 3))
  • q4 is an integer from 0 to 10 (e.g., 0, 1, 2, 3, 4, 5, 6, 7, or 8)
  • q10 is an integer from 0 to 8 (e.g., 1, 2, 3, 4, 5, or 6)
  • q11 is 0 or 1
  • Z is O or S.
  • conjugating groups can be used for conjugation to a targeting moiety through a metal-free cycloaddition:
  • q2 is an integer from 1 to 50 (e.g., an integer from 1 to 24 or from 1 to 8 (e.g., 2 or 3))
  • q4 is an integer from 0 to 10 (e.g., 0, 1, 2, 3, 4, 5, 6, 7, or 8)
  • q10 is an integer from 0 to 8 (e.g., 1, 2, 3, 4, 5, or 6)
  • q11 is 0 or 1
  • Z is O or S
  • each R M is independently H, an auxiliary moiety, —(CH 2 ) q7 —CO—N(R M1 ) 2 , or —C[—CH 2 O—(CH 2 ) q7 —CO—N(R M1 ) 2 ] 3 , where each q7 is independently an integer from 1 to 5, and each R M1 is independently H or auxiliary moiety.
  • conjugating groups can be used for conjugation to a targeting moiety through amide formation:
  • q2 is an integer from 0 to 50 (e.g., an integer from 1 to 8 (e.g., 2 or 3)), and q12 is an integer from 1 to 11 (e.g., an integer from 1 to 5 (e.g., 1, 2, 3, 4, or 5).
  • a bioreversible group is a monovalent substituent having a molecular weight of from 135 Da to 10 kDa (e.g., from 135 Da to 5 kDa, from 200 Da to 5 kDa, or from 200 Da to 2 kDa) and containing disulfide (—S—S—).
  • the shortest chain of atoms covalently linking the disulfide and the valency of the bioreversible group may be from 2 to 10 atoms (e.g., from 2 to 6 atoms or from 4 to 6 atoms (e.g., 4 or 5 atoms)).
  • the bioreversible group may be cleavable intracellularly under physiological conditions.
  • a bioreversible group may be included in phosphoesters, e.g., to reduce the overall negative charge of an immunomodulating polynucleotide of the invention.
  • the reduction in the overall negative charge of an immunomodulating polynucleotide may enhance cellular uptake of an immunomodulating polynucleotide and/or conjugate of the invention.
  • Immunomodulating polynucleotides of the invention may include one or more bioreversible groups in phosphoesters and/or abasic spacers.
  • an immunomodulating polynucleotide of the invention may include from 1 to 6 bioreversible groups (e.g., from 1 to 4 bioreversible groups (e.g., 1, 2, or 3 bioreversible groups)).
  • a bioreversible group can be of formula (XXII): R 5 —S—S-(LinkB)-, (XXII)
  • LinkB and/or R 5 includes a bulky group attached to —S—S—.
  • the inclusion of a bulky group attached to —S—S— may enhance the stability of the sulfur-sulfur bond, e.g., during the polynucleotide synthesis.
  • LinkB consists of 1, 2, or 3 groups, each of the groups being independently selected from the group consisting of optionally substituted C 1-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, optionally substituted C 6-10 arylene, optionally substituted C 2-12 heteroalkylene, and optionally substituted C 1-9 heterocyclylene.
  • LinkB and —S—S— combine to form a structure selected from the group consisting of:
  • each R 6 is independently C 2-7 alkanoyl; C 1-6 alkyl; C 2-6 alkenyl; C 2-6 alkynyl; C 1-6 alkylsulfinyl; C 6-10 aryl; amino; (C 6-10 aryl)-C 1-4 -alkyl; C 3-8 cycloalkyl; (C 3-8 cycloalkyl)-C 1-4 -alkyl; C 3-8 cycloalkenyl; (C 3-8 cycloalkenyl)-C 1-4 -alkyl; halo; C 1-9 heterocyclyl; C 1-9 heteroaryl; (C 1-9 heterocyclyl)oxy; (C 1-9 heterocyclyl)aza; hydroxy; C 1-6 thioalkoxy; —(CH 2 ) q CO 2 R A , where q is an integer from zero to four, and R A is selected from the group consisting of C 1-6 alkyl, C 6-10 aryl, and (C 6-10 ary
  • n1 0, 1, or 2;
  • n2 0, 1, 2, 3, or 4;
  • LinkC can include from 0 to 3 multivalent monomers (e.g., optionally substituted C 1-6 alkane-triyl, optionally substituted C 1-6 alkane-tetrayl, ortrivalent nitrogen atom) and one or more divalent monomers (e.g., from 1 to 40), where each divalent monomer is independently optionally substituted C 1-6 alkylene; optionally substituted C 2-6 alkenylene; optionally substituted C 2-6 alkynylene; optionally substituted C 3-8 cycloalkylene; optionally substituted C 3-8 cycloalkenylene; optionally substituted C 6-14 arylene; optionally substituted C 1-9 heteroarylene having 1 to 4 heteroatoms selected from N, O, and S; optionally substituted C 1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S; imino; optionally substituted N; O; or S(O) m , wherein m is 0, 1, or 2.
  • multivalent monomers e.g
  • each monomer is independently optionally substituted C 1-6 alkylene; optionally substituted C 3-8 cycloalkylene; optionally substituted C 3-8 cycloalkenylene; optionally substituted C 6-14 arylene; optionally substituted C 1-9 heteroarylene having 1 to 4 heteroatoms selected from N, O, and S; optionally substituted C 1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S; imino; optionally substituted N; O; or S(O) m , where m is 0, 1, or 2 (e.g., m is 2).
  • each monomer is independently optionally substituted C 1-6 alkylene; optionally substituted C 3-8 cycloalkylene; optionally substituted C 3-8 cycloalkenylene; optionally substituted C 6-14 arylene; optionally substituted C 1-9 heteroarylene having 1 to 4 heteroatoms selected from N, O, and S; optionally substituted C 1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S; optionally substituted N; O; or S(O) m , where m is 0, 1, or 2 (e.g., m is 2).
  • the non-bioreversible linker connecting the auxiliary moiety to the conjugation moiety or to the reaction product thereof can include from 2 to 500 (e.g., 2 to 300, 2 to 200, 2 to 100, or 2 to 50) of such monomers.
  • LinkC may include one or more polyethylene glycols (e.g., the polyethylene glycols may have a molecular weight of from 88 Da to 1 kDa (e.g., from 88 Da to 500 Da).
  • Non-limiting examples of -LinkC(-R M ) r include:
  • R 14 is a bond to —S—S—
  • R M is an auxiliary moiety or -Q G [(-Q B -Q C -Q D ) s2 -R M1 ] p1 ,
  • each r4 is independently an integer from 1 to 6;
  • each r5 is independently an integer from 0 to 10.
  • R M is an auxiliary moiety. In some embodiments, at least one R M1 is an auxiliary moiety.
  • the bioreversible linker group is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • one end of the group is connected to a polynucleotide and the other end is connected to a target moiety (in one embodiment, an antibody).
  • a non-bioreversible group is a monovalent substituent that does not contain bonds cleavable under physiologic conditions in serum or in an endosome (e.g., esters, thioesters, or disulfides).
  • the non-bioreversible group may be optionally substituted C 2-16 alkyl; optionally substituted C 3-16 alkenyl; optionally substituted C 3-16 alkynyl; optionally substituted C 3-8 cycloalkyl; optionally substituted C 3-8 cycloalkenyl; optionally substituted (C 3-8 cycloalkyl)-C 1-4 -alkyl; optionally substituted (C 3-8 cycloalkenyl)-C 1-4 -alkyl; optionally substituted C 6-14 aryl; optionally substituted (C 6-14 aryl)-C 1-4 -alkyl; optionally substituted C 1-9 heteroaryl having 1 to 4 heteroatoms selected from N, O, and S; optionally substituted (C 1-9
  • a non-bioreversible phosphotriester may be a phosphate or a phosphorothioate substituted with a substituent that is a conjugating group, C 2-6 alkyl,
  • n is an integer from 1 to 6;
  • R 9 is optionally substituted C 6 aryl; optionally substituted C 4-5 heteroaryl that is a six member ring containing 1 or 2 nitrogen atoms; or optionally substituted C 4-5 heterocyclyl that is a six member ring containing 1 or 2 nitrogen atoms;
  • R 10 is H or C 1-6 alkyl
  • R 11 is a halogen, —COOR 11A , or —CON(R 11B ) 2 , where each of R 11A and R 11B is independently H, optionally substituted C 1-6 alkyl, optionally substituted C 6-14 aryl, optionally substituted C 1-9 heteroaryl, or optionally substituted C 2-9 heterocyclyl; and
  • the azido-containing substrate is N-(2-amino-containing substrate
  • a non-bioreversible group is -LinkD(-R M1 ) r1 , where LinkD is a multivalent linker, each R M1 is independently H or an auxiliary moiety, and r1 is an integer from 1 to 6.
  • -LinkD(-R M1 ) r1 is of formula (XXIV): -Q R -Q 3 ([-Q 4 -Q 5 -Q 6 ] r2 -Q 7 -R M1 ) r1 , (XXIV)
  • r1 is an integer from 1 to 6;
  • each r2 is independently an integer from 0 to 50 (e.g., from 0 to 30), where the repeating units are same or different;
  • Q R is [-Q 4 -Q 5 -Q 6 ] r2 -Q L -, where Q L is optionally substituted C 2-12 heteroalkylene (e.g., a heteroalkylene containing —C(O)—N(H)—, —N(H)—C(O)—, —S(O) 2 —N(H)—, or —N(H)—S(O) 2 —), optionally substituted C 1-12 thioheterocyclylene
  • C 1-12 heterocyclylene e.g., 1,2,3-triazole-1,4-diyl or
  • Q 3 is a linear group (e.g., [-Q 4 -Q 5 -Q 6 ] r2 -), if r1 is 1, or a branched group (e.g., [-Q 4 -Q 5 -Q 6 ] s -Q 8 ([-Q 4 -Q 5 -Q 6 ] r2 -(Q 8 ) r3 ) r4 , where r3 is 0 or 1, r4 is 0, 1, 2, or 3), if r1 is an integer from 2 to 6; each r2 is independently an integer from 0 to 50 (e.g., from 0 to 30), where the repeating units are the same or different;
  • each Q 4 and each Q 6 is independently absent —CO—, —NH—, —O—, —S—, —SO 2 —, —OC(O)—, —COO—, —NHC(O)—, —C(O)NH—, —CH 2 —, —CH 2 NH—, —NHCH 2 —, —CH 2 O—, or —OCH 2 —;
  • each Q 5 is independently absent, optionally substituted C 1-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, optionally substituted C 2-12 heteroalkylene, or optionally substituted C 1-9 heterocyclylene;
  • each Q 7 is independently absent, —CO—, —NH—, —O—, —S—, —SO 2 —, —CH 2 —, —C(O)O—, —OC(O)—, —C(O)NH—, —NH—C(O)—, —NH—CH(R a )—C(O)—, or —C(O)—CH(R a )—NH—;
  • each Q 8 is independently optionally substituted C 1-6 alkane-triyl, optionally substituted C 1-6 alkane-tetrayl, optionally substituted C 2-6 heteroalkane-triyl, or optionally substituted C 2-6 heteroalkane-tetrayl;
  • each R a is independently H or an amino acid side chain
  • each R M1 is independently H or an auxiliary moiety.
  • LinkD may include a single branching point, if each r3 is 0, or multiple branching points, if at least one r3 is 1.
  • Q R may be -Q 5 -Q 4 -Q L -, where Q 5 is optionally substituted C 2-12 heteroalkylene or optionally substituted C 1-12 alkylene, and Q 4 is —CO—, —NH—, or —O—.
  • Q L may be:
  • Q 3 may be a linear group of formula [-Q 4 -Q 5 -Q 6 ] r2 -, where Q 4 , Q 5 , and Q 6 are as defined for formula (XXIV).
  • Q 3 may be a branched group [-Q 4 -Q 5 -Q 6 ] r2 -Q 8 ([-Q 4 -Q 5 -Q 6 ] r2 -(Q 8 ) r3 ) r4 , where each Q 8 is independently optionally substituted C 1-6 alkane-triyl, optionally substituted C 1-6 alkane-tetrayl, optionally substituted C 2-6 heteroalkane-triyl, or optionally substituted C 2-6 heteroalkane-tetrayl;
  • each r2 is independently an integer from 0 to 50 (e.g., from 0 to 30), where the repeating units are the same or different;
  • r3 is 0 or 1;
  • r4 is 0, 1, 2, or 3;
  • r3 is 0.
  • Q 8 is:
  • the non-bioreversible linker group is N-bioreversible linker group
  • one end of the group is connected to a polynucleotide and the other end is connected to a target moiety (in one embodiment, an antibody).
  • An auxiliary moiety is a monovalent group containing a dye or a hydrophilic group or a combination thereof (e.g., a hydrophilic polymer (e.g., polyethylene glycol) (PEG)), a positively charged polymer (e.g., polyethylene imine)), or a sugar alcohol (e.g., glucitol)).
  • An auxiliary moiety may have a theoretical molecular weight of from 100 Da to 2.5 kDa (e.g., from 350 Da to 2.5 kDa, from 100 Da to 1,200 Da, or from 1 kDa to 2.5 kDa).
  • Dyes may be included in the phosphoester groups for the purpose of visualization of uptake or monitoring the movement of the conjugates of the invention inside a cell (e.g., using Fluorescence Recovery After Photobleaching (FRAP)). Dyes known in the art may be included as an auxiliary moiety linked to the polynucleotide via a phosphate or phosphorothioate at the 5′- or 3′-terminus or via a phosphate or phosphorothioate bonding two consecutive nucleosides together.
  • FRAP Fluorescence Recovery After Photobleaching
  • Non-limiting examples of useful structures that can be used as dyes include FITC, RD1, allophycocyanin (APC), aCFTM dye (Biotium, Hayward, Calif.), BODIPY (InvitrogenTM 10 of Life Technologies, Carlsbad, Calif.), AlexaFluor® (InvitrogenTM of Life Technologies, Carlsbad, Calif.), DyLight Fluor (Thermo Scientific Pierce Protein Biology Products, Rockford, Ill.), ATTO (ATTO-TEC GmbH, Siegen, Germany), FluoProbe (Interchim SA, Motlugon, France), and Abberior Probes (Abberior GmbH, Gottingen, Germany).
  • Hydrophilic polymers and positively charged polymers that may be used as auxiliary moieties in the immunomodulating polynucleotides of the invention and in the conjugates of the invention are known in the art.
  • a non-limiting example of a hydrophilic polymer is polyethylene glycol).
  • a non-limiting example of a positively charged polymer is polyethylene imine).
  • a sugar alcohol-based auxiliary moiety may be, e.g., amino-terminated glucitol or a glucitol cluster.
  • the amino-terminated glucitol auxiliary moiety is:
  • Non-limiting examples of glucitol clusters are:
  • a compound of Formula (B) R x -L N -(Q) e (B) or a stereoisomer, a mixture of two or more diastereomers, a tautomer, or a mixture of two or more tautomers; or a pharmaceutically acceptable salt, solvate, or hydrate thereof; wherein:
  • R x is a conjugating group
  • L N is a linker
  • each Q is independently an oligonucleotide comprising a phosphotriester
  • e is an integer of 1, 2, 3, or 4.
  • R x is
  • L N is a linker comprising a polyethylene glycol.
  • L N is
  • d is an integer ranging from about 0 to about 50. In certain embodiments, d is an integer ranging from about 0 to about 10. In certain embodiments, d is an integer ranging from about 0 to about 5. In certain embodiments, d is an integer of about 0, about 1, or about 3.
  • e is an integer of 1.
  • each Q independently has the structure of Formula (D):
  • X N , X 3′ , X 5′ , Y P , b, and c are each as defined herein.
  • the targeting moieties used in the conjugates of the invention can be used to target specific cells and tissues in a body for targeted delivery of the conjugated payload polynucleotide.
  • the cells targeted by the conjugates of the invention are professional APCs (e.g., B cells, pDCs, or macrophages).
  • the targeting moiety can be an antigen-binding moiety (e.g., an antibody or antigen-binding fragment thereof), a polypeptide, an aptamer, or a group including one or more small molecules (e.g., mannose).
  • the targeting moieties in the conjugates of the invention can be effective in addressing the problem of the uneven tissue distribution of of immunomodulating polynucleotides in vivo.
  • An antigen-binding moiety in the conjugate of the invention can be an antibody or an antigen-binding fragment thereof (e.g., F(ab) 2 or Fab) or an engineered derivative thereof (e.g., Fcab or a fusion protein (e.g., scFv)).
  • a human or chimeric (e.g., humanized) antibody can be used as an antibody in the conjugate of the invention.
  • the antigen-binding moiety targets the cells having the surface antigen that is recognized by the antigen-binding moiety.
  • APCs can be targeted by the antigen-binding moieties in the conjugates of the invention.
  • B cells can be targeted by anti-CD38, anti-CD79b, anti-CD30, anti-CD22, or anti-CD20, anti-CD19 antibodies or antigen-binding fragments thereof or engineered derivatives thereof.
  • Plasmacytoid dendritic cells pDCs
  • Macrophages can be targeted by anti-CD163, anti-CD40, anti-CD74, anti-CD206, or anti-CD123 antibodies or antigen-binding fragments thereof or engineered derivatives thereof.
  • Non-limiting examples of anti-CD38 antibodies are daratumumab, SAR650984, MOR202, or any one of antibodies Ab79, Ab19, Ab43, Ab72, and Ab110 disclosed in WO 2012/092616, the disclosure of these antibodies is incorporated herein by reference.
  • a non-limiting example of an anti-CD79b antibody is huMA79b v28 disclosed in WO 2014/011521.
  • a non-limiting example of an anti-CD22 antibody is 10F4 disclosed in US 2014/0127197.
  • a non-limiting example of an anti-CD20 antibody is rituximab.
  • a non-limiting example of an anti-DEC205 antibody is provided in US 2010/0098704, the antibodies of which are incorporated herein by reference.
  • Non-limiting examples of anti-CD40 antibodies are lucatumumab and dacetuzumab.
  • a non-limiting example of of an anti-CD304 antibody is vesencumab.
  • the targeting moiety can be a polypeptide having an affinity for cells (e.g., having an affinity for a cell type, e.g., a plasmacytoid cell).
  • polypeptides are RGD peptide, rabies virus glycoprotein (RVG), and a DC3 peptide.
  • the targeting moiety can be a small molecule capable of complexing a receptor expressed on the surface of the targeted cell.
  • small molecules that may be used as targeting moieties in the conjugates of the invention are folate, mannose, PSMA ligand, and mannose clusters.
  • Folate may be used as a targeting moiety.
  • folate may be of the following structure:
  • Mannose or a mannose cluster can be used to target the conjugates of the invention to plasmacytoid dendritic cells and macrophages, as these cells express mannose receptor on their surface.
  • Mannose clusters are known in the art.
  • the mannose auxiliary moiety e.g., a mannose cluster
  • the mannose auxiliary moiety may be of formula (XXV): -(-Q M1 -Q M2 -Q M3 -) s3 -Q M4 [(-Q M1 -Q M2 -Q M3 -) s3 -Q M5 ] p3 , (XXV)
  • p3 is 1, 2, or 3;
  • each s3 is independently an integer from 0 to 50 (e.g., from 0 to 30);
  • each Q M1 and each Q M3 is independently absent, —CO—, —NH—, —O—, —S—, —SO 2 —, —OC(O)—, —COO—, —NHC(O)—, —C(O)NH—, —CH 2 —, —CH 2 NH—, —NHCH 2 —, —CH 2 O—, or —OCH 2 —; and
  • each Q M2 is independently absent, optionally substituted C 1-12 alkylene, optionally substituted C 2-12 alkenylene, optionally substituted C 2-12 alkynylene, optionally substituted C 2-12 heteroalkylene, or optionally substituted C 1-9 heterocyclylene;
  • Q M4 is absent (if p3 is 1), optionally substituted C 1-6 alkane-triyl (if p3 is 2), optionally substituted C 1-6 alkane-tetrayl (if p3 is 3), optionally substituted C 2-6 heteroalkane-triyl (if p3 is 2), or optionally substituted C 2-6 heteroalkane-tetrayl (if p3 is 3);
  • each Q M5 is independently mannose or -Q M6 [(-Q M1 -Q M2 -Q M3 ) s2 -R M2 ] p1 , where each R M2 is independently mannose;
  • each Q M6 is independently optionally substituted C 1-6 alkane-triyl, optionally substituted C 1-6 alkane-tetrayl, optionally substituted C 2-6 heteroalkane-triyl, or optionally substituted C 2-6 heteroalkane-tetrayl.
  • mannose clusters are:
  • Ab is an antibody. In certain embodiments, in Formula (C), Ab is a monoclonal antibody.
  • f is an integer of 1 or 2. In certain embodiments, in Formula (C), f is an integer of 1.
  • both e and f are each an integer of 1.
  • DAR refers to a drug-antibody ratio of a CpG antibody conjugate, more specifically a polynucleotide-antibody ratio.
  • the CpG antibody conjugate has a DAR ranging from about 1 to about of about 20, from about 1 to about 10, from about 1 to about 8, from about 1 to about 4, or from about 1 to about 2.
  • the CpG antibody conjugate has a DAR of about 1, about 2, about 3, about 4, about 5, about 6, about 7, or about 8.
  • Reactions useful for conjugating a targeting moiety to one or more immunomodulating polynucleotides are described herein and are known in the art (e.g., bioorthogonal reactions).
  • Exemplary reactions that can be used to form this bond include Hüisgen cycloaddition (metal-catalyzed or metal-free) between an azido and an alkyne-based conjugating group (e.g., optionally substituted C 6-16 heterocyclylene containing an endocyclic carbon-carbon triple bond or optionally substituted C 8-16 cycloalkynyl) to form a triazole moiety; the Diels-Alder reaction between a dienophile and a diene/hetero-diene; bond formation via other pericyclic reactions such as the ene reaction; amide orthioamide bond formation; sulfonamide bond formation (e.g., with azido compounds); alcohol or phenol alkylation (e.g., Williamson alkylation),
  • the conjugation reaction is a dipolar cycloaddition
  • the conjugation moiety includes azido, optionally substituted C 6-16 heterocyclylene containing an endocyclic carbon-carbon triple bond, or optionally substituted C 8-16 cycloalkynyl.
  • the complementary reactive group and the conjugating group are selected for their mutual complementarity. For example, an azide may be used in one of the conjugating group and the complementary reactive group, while an alkyne may be used in the other of the conjugating group and the complementary reactive group.
  • Nucleophiles and electrophiles can engage in bond forming reactions selected from, without limitation, insertion by an electrophile into a C—H bond, insertion by an electrophile into an O—H bond, insertion by an electrophile into an N—H bond, addition of the electrophile across an alkene, addition of the electrophile across an alkyne, addition to electrophilic carbonyl centers, substitution at electrophilic carbonyl centers, addition to ketenes, nucleophilic addition to isocyanates, nucleophilic addition to isothiocyanates, nucleophilic substitution in electrophilic silyl groups, nucleophilic displacement of a leaving group (e.g., a halide or a pseudohalide) in an alkyl halide or pseudohalide; nucleophilic addition/elimination at a carbonyl of an activated carboxylic acid ester (e.g., PFP ester or TFP ester), thioester, anhydride, or acyl
  • a nucleophilic conjugating group can be optionally substituted alkene, optionally substituted alkyne, optionally substituted aryl, optionally substituted heterocyclyl, hydroxyl, amino, alkylamino, anilido, orthio.
  • An electrophilic conjugating group can be azide, activated carbonyl (e.g., activated carboxylic acid ester (e.g., succinimidyl ester or sulfosuccinimidyl ester), thioester, anhydride, or acyl halide), isocyanate, thioisocyanate, Michael acceptor (e.g., maleimide), alkyl halide or pseudohalide, epoxide, episulfide, aziridine, or electron-deficient aryl.
  • activated carbonyl e.g., activated carboxylic acid ester (e.g., succinimidyl ester or sulfosuccinimidyl ester), thioester, anhydride, or acyl halide
  • isocyanate e.g., thioisocyanate
  • Michael acceptor e.g., maleimide
  • alkyl halide or pseudohalide e
  • conjugation can occur via a condensation reaction to form a linkage that is a hydrazone bond.
  • Conjugation can involve the formation of an amide bond, e.g., by activation of a carboxyl-based conjugating group (e.g., carboxylic acid, ester, or —CONH 2 ) and subsequent reaction with a primary amine in a conjugating group.
  • a carboxyl-based conjugating group e.g., carboxylic acid, ester, or —CONH 2
  • Activating agents can be various carbodiimides like: EDC (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride), EDAC (1-ethyl-3(3-dimethylaminopropyl)carbodiimide hydrochloride), DCC (dicyclohexyl carbodiimide), CMC (1-Cyclohexyl-3-(2-morpholinoethyl) carbodiimide), DIC (diisopropyl carbodiimide) or Woodward's reagent K (N-ethyl-3-phenylisoxazolium-3′-sulfonate).
  • Activation of the carboxyl-based conjugating group that is —CONH 2 can be achieved using a transglutaminase. Reaction of an activated NHS-Ester-based conjugating group with a primary amine-based conjugating group also results in formation of an amide bond.
  • the polynucleotide may contain a carbonyl-based conjugating group.
  • Conjugation with concomitant formation of a secondary amine can be achieved through reductive amination (i.e., by reacting an amine-based conjugating group with an aldehyde-based conjugating group, followed by a reduction with a hydride donor (e.g., sodium cyanoborohydride or sodium triacetoxyborohydride)).
  • a hydride donor e.g., sodium cyanoborohydride or sodium triacetoxyborohydride
  • Ether formation can also be used to conjugate a targeting moiety to one or more polynucleotides to form a conjugate of the invention.
  • Ether linkage formation can involve a reaction between an epoxide-based conjugating group with a hydroxy-based conjugating group.
  • Thiols can also be used as conjugating groups.
  • conjugation via the formation of disulfide bonds can be accomplished by pyridyldisulfide mediated thiol-disulfide exchange.
  • Introduction of sulfhydryl-based conjugating groups is mediated for instance by Traut's Reagent (2-iminothiolane) SATA (N-succinimidyl S-acetylthioacetate, SATP (succinimidyl acetylthiopropionate), SPDP (N-succinimidyl 3-(2-pyridyldithio)propionate, SMPT (succinimidyloxycarbonyl- ⁇ -methyl- ⁇ -(2-pyridyldithio)toluene), N-acetylhomocysteinethiolactone, SAMSA (S-acetylmercaptosuccinic anhydride), AMBH (2-Acedamid
  • Thioether linkage formation can be performed by reacting a sulfhydryl based conjugating groups with maleimide- or iodoacetyl-based conjugating groups or by reacting with epoxide-based conjugating groups.
  • Maleimide-based conjugating groups can be introduced by SMCC (succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate), sulfo-SMCC (sulfosuccinimidyl 4-(N-maleidomethyl)-cyclohexane-1-carboxylate), MBS (m-Maleimidobenzoyl-N-hydroxysuccinimide ester), sulfo-MBS (m-Maleimidobenzoyl-N-sulfohydroxy succinimide ester), SMPB (Succinimidyl-4-(p-maleidophenyl)butyrate), sulfo-SMPB (sulfosuccinimidyl 4-(p-maleimidophenyl)butyrate), GMBS (N- ⁇ -maleimidobuturyl-oxysuccinimide ester), sulfo GMBS (N- ⁇ -
  • Conjugation via the formation of a carbamate linkage can be performed by reaction of a hydroxy-based conjugating groups with CDI (N,N′-carbonyldiimidazole) or DSC (N,N′-disuccinimidyl carbonate) or N-hydroxysuccinimidylchloroformate and subsequent reaction with an amine-based conjugating group.
  • CDI N,N′-carbonyldiimidazole
  • DSC N,N′-disuccinimidyl carbonate
  • N-hydroxysuccinimidylchloroformate N-hydroxysuccinimidylchloroformate
  • Cycloaddition reactions can be used to form the desired covalent bond.
  • Representative cycloaddition reactions include, but are not limited to, the reaction of an alkene-based conjugating group with a 1,3-diene-based conjugating group (Diels-Alder reaction), the reaction of an alkene-based conjugating group with an ⁇ , ⁇ -unsaturated carbonyl-based conjugating group (hetero Diels-Alder reaction), and the reaction of an alkyne-based conjugating group with an azido-based conjugating group (Hüisgen cycloaddition, including metal-catalyzed and metal-free variants thereof) to afford a triazole moiety.
  • conjugating groups that include reactants for cycloaddition reactions are: alkenes, alkynes, 1,3-dienes, ⁇ , ⁇ -unsaturated carbonyls, and azides.
  • alkenes alkynes
  • 1,3-dienes 1,3-dienes
  • ⁇ , ⁇ -unsaturated carbonyls 1,3-dienes
  • azides azides
  • Hüisgen cycloaddition (click reaction) between azides and alkynes has been used for the functionalization of diverse biological entities.
  • Strained alkyne-based conjugating group is a carbocyclic or heterocyclic ring system including one endocyclic carbon-carbon triple bond (e.g., optionally substituted C 6-16 heterocyclylene containing an endocyclic carbon-carbon triple bond or optionally substituted C 8-16 cycloalkynyl).
  • Strained alkyne-based conjugating groups can be useful for conjugating a targeting moiety to a polynucleotide through metal-free dipolar cycloadditions with an azido conjugating group.

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